From degironc at sissa.it Thu May 1 00:52:19 2008 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 01 May 2008 00:52:19 +0200 Subject: [Pw_forum] difference between nr1 and nrx1 In-Reply-To: <4818DD44.6050807@mit.edu> References: <4818DD44.6050807@mit.edu> Message-ID: <4818F823.1020202@sissa.it> Dear Timo, due to memory access conflicts for certain architectures (cray was one of these) FFT routines were significantly slower if some of the nrx1,nrx2,nrx3 (nr1 in scalar and nr3 in parallel executions) was a multiple of 2 while obviously nr1,nr2,nr3 are best when they are powers of 2. It was therefore convenient to have the flexibility to set nrx1=nr1+1 (or nrx3=nr3+1) when nr1(nr3) was even. Now this is not anymore the case on most machines but the distinction between nr? and nrx? remains and in some case it is still useful. Best regards, Stefano de Gironcoli Timo Thonhauser wrote: > Dear Developers, > > What is the difference between nr1, nr2, nr3 and nrx1, nrx2, nrx3 > in the code? For all practical purposes they always seem to be > the same. > > In PW/pwcom.f90 we find: > > nr1, &! fft dimension along x > nr2, &! fft dimension along y > nr3, &! fft dimension along z > nrx1, &! maximum fft dimension along x > nrx2, &! maximum fft dimension along y > nrx3, &! maximum fft dimension along z > > But when would nr1 differ from nrx1? > > Thanks a lot! > Timo > > From degironc at sissa.it Thu May 1 00:59:40 2008 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 01 May 2008 00:59:40 +0200 Subject: [Pw_forum] difference between nr1 and nrx1 In-Reply-To: <4818F823.1020202@sissa.it> References: <4818DD44.6050807@mit.edu> <4818F823.1020202@sissa.it> Message-ID: <4818F9DC.4020901@sissa.it> just to complete the information, this check is done in the good_fft_dimension function in Modules/fft_scalar.f90 stefano Stefano de Gironcoli wrote: > Dear Timo, > due to memory access conflicts for certain architectures (cray was > one of these) FFT routines were significantly slower if some of the > nrx1,nrx2,nrx3 (nr1 in scalar and nr3 in parallel executions) was a > multiple of 2 while obviously nr1,nr2,nr3 are best when they are powers > of 2. It was therefore convenient to have the flexibility to set > nrx1=nr1+1 (or nrx3=nr3+1) when nr1(nr3) was even. > Now this is not anymore the case on most machines but the distinction > between nr? and nrx? remains and in some case it is still useful. > Best regards, > Stefano de Gironcoli > > Timo Thonhauser wrote: > >> Dear Developers, >> >> What is the difference between nr1, nr2, nr3 and nrx1, nrx2, nrx3 >> in the code? For all practical purposes they always seem to be >> the same. >> >> In PW/pwcom.f90 we find: >> >> nr1, &! fft dimension along x >> nr2, &! fft dimension along y >> nr3, &! fft dimension along z >> nrx1, &! maximum fft dimension along x >> nrx2, &! maximum fft dimension along y >> nrx3, &! maximum fft dimension along z >> >> But when would nr1 differ from nrx1? >> >> Thanks a lot! >> Timo >> >> >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From thonhauser at MIT.EDU Thu May 1 16:14:30 2008 From: thonhauser at MIT.EDU (Timo Thonhauser) Date: Thu, 01 May 2008 10:14:30 -0400 Subject: [Pw_forum] difference between nr1 and nrx1 In-Reply-To: References: Message-ID: <4819D046.4000306@mit.edu> Dear Stefano, Thanks - that helped a lot! However, I have one more question: I have to scan and work with the density in such a way that I want to know the real space position of each grid point. So what I do is: ifft = 0 do zfft=0, nr3-1 do yfft=0, nr2-1 do xfft=0, nr1-1 ! ifft = ifft + 1 rho = rho_val(ifft,1) + rho_core(ifft) ... r_pos(ifft,1) = dble(xfft)/dble(nr1) r_pos(ifft,2) = dble(yfft)/dble(nr2) r_pos(ifft,3) = dble(zfft)/dble(nr3) ! end do end do end do Say, we are running the code on a gray and nrx1 was different from nr1. The loop over xfft above would stay the same and there is not need to let it run over xfft=0 to nrx1-1, right? As I understand it, the nrx? are only constructs to make the fft easier on certain machines, but there are no extra real space density grid points associated with them. If we use only one processor then nr1*nr2*nr3 = nrxx and the charge density is defined as rho(1:nrxx). But if nr? is different from nrx? then nrx1*nrx2*nrx3 IS NOT nrxx, but yet the charge density still only has rho(1:nrxx) values, right? Thanks for all you help! Best, Timo pw_forum-request at pwscf.org wrote: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. Re: difference between nr1 and nrx1 (Stefano de Gironcoli) > 2. Re: difference between nr1 and nrx1 (Stefano de Gironcoli) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 01 May 2008 00:52:19 +0200 > From: Stefano de Gironcoli > Subject: Re: [Pw_forum] difference between nr1 and nrx1 > To: PWSCF Forum > Message-ID: <4818F823.1020202 at sissa.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear Timo, > due to memory access conflicts for certain architectures (cray was > one of these) FFT routines were significantly slower if some of the > nrx1,nrx2,nrx3 (nr1 in scalar and nr3 in parallel executions) was a > multiple of 2 while obviously nr1,nr2,nr3 are best when they are powers > of 2. It was therefore convenient to have the flexibility to set > nrx1=nr1+1 (or nrx3=nr3+1) when nr1(nr3) was even. > Now this is not anymore the case on most machines but the distinction > between nr? and nrx? remains and in some case it is still useful. > Best regards, > Stefano de Gironcoli > > Timo Thonhauser wrote: > >> Dear Developers, >> >> What is the difference between nr1, nr2, nr3 and nrx1, nrx2, nrx3 >> in the code? For all practical purposes they always seem to be >> the same. >> >> In PW/pwcom.f90 we find: >> >> nr1, &! fft dimension along x >> nr2, &! fft dimension along y >> nr3, &! fft dimension along z >> nrx1, &! maximum fft dimension along x >> nrx2, &! maximum fft dimension along y >> nrx3, &! maximum fft dimension along z >> >> But when would nr1 differ from nrx1? >> >> Thanks a lot! >> Timo >> >> >> > > > > ------------------------------ > > Message: 2 > Date: Thu, 01 May 2008 00:59:40 +0200 > From: Stefano de Gironcoli > Subject: Re: [Pw_forum] difference between nr1 and nrx1 > To: PWSCF Forum > Message-ID: <4818F9DC.4020901 at sissa.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > just to complete the information, this check is done in the > good_fft_dimension function in Modules/fft_scalar.f90 > stefano > > Stefano de Gironcoli wrote: > >> Dear Timo, >> due to memory access conflicts for certain architectures (cray was >> one of these) FFT routines were significantly slower if some of the >> nrx1,nrx2,nrx3 (nr1 in scalar and nr3 in parallel executions) was a >> multiple of 2 while obviously nr1,nr2,nr3 are best when they are powers >> of 2. It was therefore convenient to have the flexibility to set >> nrx1=nr1+1 (or nrx3=nr3+1) when nr1(nr3) was even. >> Now this is not anymore the case on most machines but the distinction >> between nr? and nrx? remains and in some case it is still useful. >> Best regards, >> Stefano de Gironcoli >> >> Timo Thonhauser wrote: >> >> >>> Dear Developers, >>> >>> What is the difference between nr1, nr2, nr3 and nrx1, nrx2, nrx3 >>> in the code? For all practical purposes they always seem to be >>> the same. >>> >>> In PW/pwcom.f90 we find: >>> >>> nr1, &! fft dimension along x >>> nr2, &! fft dimension along y >>> nr3, &! fft dimension along z >>> nrx1, &! maximum fft dimension along x >>> nrx2, &! maximum fft dimension along y >>> nrx3, &! maximum fft dimension along z >>> >>> But when would nr1 differ from nrx1? >>> >>> Thanks a lot! >>> Timo >>> >>> >>> >>> >> _______________________________________________ >> 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 > > > End of Pw_forum Digest, Vol 11, Issue 1 > *************************************** > -- ______________________________________________________________________ Dr. TIMO THONHAUSER Department of Materials Science and Engineering (617) 253 6026 MIT, 13-4084, 77 Massachusetts Avenue thonhauser at mit.edu Cambridge, MA 02139-4307, USA www.mit.edu/~thonhaus ______________________________________________________________________ From degironc at sissa.it Thu May 1 17:23:12 2008 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 01 May 2008 17:23:12 +0200 Subject: [Pw_forum] difference between nr1 and nrx1 In-Reply-To: <4819D046.4000306@mit.edu> References: <4819D046.4000306@mit.edu> Message-ID: <4819E060.5070301@sissa.it> Dear Timo, the nrxx is the real dimension of the FFT array that in a scalar run in nrx1*nrx2*nrx3 and in a parallel run is nrx1*nrx2* dfftp%npp(me_pool+1) where npp(me_pool+1) is the number of fft x-y planes belonging to the processor me_pool in a given pool. In case nrx1/=nr1 there are extra positions in the array that usually contain zeros although is it safer not counting on that. In order to do the operation you describe we typically would do something like === #if defined (__PARA) idx0 = nrx1*nrx2 * SUM ( dfftp%npp(1:me_pool) ) #else idx0 = 0 #endif DO ifft = 1, nrxx ! ... define three indices (xfft,yfft,zfft) idx = idx0 + ifft - 1 zfft = idx / (nrx1*nrx2) idx = idx - (nrx1*nrx2)*zfft yfft = idx / nrx1 idx = idx - nrx1*yfft xfft = idx ! ! ... do not include points outside the physical range ! IF ( xfft >= nr1 .or. yfft >= nr2 .or. zfft >= nr3 ) CYCLE rho = rho_val(ifft,1) + rho_core(ifft) r_pos(ifft,1) = dble(xfft)/dble(nr1) r_pos(ifft,2) = dble(yfft)/dble(nr2) r_pos(ifft,3) = dble(zfft)/dble(nr3) ! END DO ==== that also works in parallel (see for instance subroutine qpointlist in PW/realus or PW/make_pointlist.f90) If you need to access the whole density in a random access way, as for instance in the symmetrization of the charge density, this is problematic due to the fact that the density is distributed and the only simple strategy we found was to collect all density slices in a local array (dimensioned nrx1*nrx2*nrx3) and perform the symmetrization in scalar mode.... you can see the gather/symmetrize/scatter procedure in PW/psymrho.f90 routine... obviously this is fine because the symmetrization is not computationally intensive and therefore we do not loose too much in doing it in scalar but in other situations other strategies may be needed. hope this helps, stefano Timo Thonhauser wrote: > Dear Stefano, > > Thanks - that helped a lot! However, I have one more question: > I have to scan and work with the density in such a way that > I want to know the real space position of each grid point. > So what I do is: > > ifft = 0 > > do zfft=0, nr3-1 > do yfft=0, nr2-1 > do xfft=0, nr1-1 > ! > ifft = ifft + 1 > rho = rho_val(ifft,1) + rho_core(ifft) > > ... > > r_pos(ifft,1) = dble(xfft)/dble(nr1) > r_pos(ifft,2) = dble(yfft)/dble(nr2) > r_pos(ifft,3) = dble(zfft)/dble(nr3) > ! > end do > end do > end do > > Say, we are running the code on a gray and nrx1 was different > from nr1. The loop over xfft above would stay the same and there > is not need to let it run over xfft=0 to nrx1-1, right? > > As I understand it, the nrx? are only constructs to make the > fft easier on certain machines, but there are no extra real > space density grid points associated with them. If we use only > one processor then nr1*nr2*nr3 = nrxx and the charge density is > defined as rho(1:nrxx). But if nr? is different from nrx? then > nrx1*nrx2*nrx3 IS NOT nrxx, but yet the charge density still > only has rho(1:nrxx) values, right? > > Thanks for all you help! > > Best, Timo > > > > > pw_forum-request at pwscf.org wrote: > >> Send Pw_forum mailing list submissions to >> pw_forum at pwscf.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://www.democritos.it/mailman/listinfo/pw_forum >> or, via email, send a message with subject or body 'help' to >> pw_forum-request at pwscf.org >> >> You can reach the person managing the list at >> pw_forum-owner at pwscf.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Pw_forum digest..." >> >> >> Today's Topics: >> >> 1. Re: difference between nr1 and nrx1 (Stefano de Gironcoli) >> 2. Re: difference between nr1 and nrx1 (Stefano de Gironcoli) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Thu, 01 May 2008 00:52:19 +0200 >> From: Stefano de Gironcoli >> Subject: Re: [Pw_forum] difference between nr1 and nrx1 >> To: PWSCF Forum >> Message-ID: <4818F823.1020202 at sissa.it> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> Dear Timo, >> due to memory access conflicts for certain architectures (cray was >> one of these) FFT routines were significantly slower if some of the >> nrx1,nrx2,nrx3 (nr1 in scalar and nr3 in parallel executions) was a >> multiple of 2 while obviously nr1,nr2,nr3 are best when they are powers >> of 2. It was therefore convenient to have the flexibility to set >> nrx1=nr1+1 (or nrx3=nr3+1) when nr1(nr3) was even. >> Now this is not anymore the case on most machines but the distinction >> between nr? and nrx? remains and in some case it is still useful. >> Best regards, >> Stefano de Gironcoli >> >> Timo Thonhauser wrote: >> >> >>> Dear Developers, >>> >>> What is the difference between nr1, nr2, nr3 and nrx1, nrx2, nrx3 >>> in the code? For all practical purposes they always seem to be >>> the same. >>> >>> In PW/pwcom.f90 we find: >>> >>> nr1, &! fft dimension along x >>> nr2, &! fft dimension along y >>> nr3, &! fft dimension along z >>> nrx1, &! maximum fft dimension along x >>> nrx2, &! maximum fft dimension along y >>> nrx3, &! maximum fft dimension along z >>> >>> But when would nr1 differ from nrx1? >>> >>> Thanks a lot! >>> Timo >>> >>> >>> >>> >> >> ------------------------------ >> >> Message: 2 >> Date: Thu, 01 May 2008 00:59:40 +0200 >> From: Stefano de Gironcoli >> Subject: Re: [Pw_forum] difference between nr1 and nrx1 >> To: PWSCF Forum >> Message-ID: <4818F9DC.4020901 at sissa.it> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> just to complete the information, this check is done in the >> good_fft_dimension function in Modules/fft_scalar.f90 >> stefano >> >> Stefano de Gironcoli wrote: >> >> >>> Dear Timo, >>> due to memory access conflicts for certain architectures (cray was >>> one of these) FFT routines were significantly slower if some of the >>> nrx1,nrx2,nrx3 (nr1 in scalar and nr3 in parallel executions) was a >>> multiple of 2 while obviously nr1,nr2,nr3 are best when they are powers >>> of 2. It was therefore convenient to have the flexibility to set >>> nrx1=nr1+1 (or nrx3=nr3+1) when nr1(nr3) was even. >>> Now this is not anymore the case on most machines but the distinction >>> between nr? and nrx? remains and in some case it is still useful. >>> Best regards, >>> Stefano de Gironcoli >>> >>> Timo Thonhauser wrote: >>> >>> >>> >>>> Dear Developers, >>>> >>>> What is the difference between nr1, nr2, nr3 and nrx1, nrx2, nrx3 >>>> in the code? For all practical purposes they always seem to be >>>> the same. >>>> >>>> In PW/pwcom.f90 we find: >>>> >>>> nr1, &! fft dimension along x >>>> nr2, &! fft dimension along y >>>> nr3, &! fft dimension along z >>>> nrx1, &! maximum fft dimension along x >>>> nrx2, &! maximum fft dimension along y >>>> nrx3, &! maximum fft dimension along z >>>> >>>> But when would nr1 differ from nrx1? >>>> >>>> Thanks a lot! >>>> Timo >>>> >>>> >>>> >>>> >>>> >>> _______________________________________________ >>> 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 >> >> >> End of Pw_forum Digest, Vol 11, Issue 1 >> *************************************** >> >> > > From giannozz at nest.sns.it Thu May 1 17:40:58 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 1 May 2008 17:40:58 +0200 Subject: [Pw_forum] difference between nr1 and nrx1 In-Reply-To: <4819D046.4000306@mit.edu> References: <4819D046.4000306@mit.edu> Message-ID: On May 1, 2008, at 16:14 , Timo Thonhauser wrote: > As I understand it, the nrx? are only constructs to make the > fft easier on certain machines, but there are no extra real > space density grid points associated with them. If we use only > one processor then nr1*nr2*nr3 = nrxx and the charge density is > defined as rho(1:nrxx). But if nr? is different from nrx? then > nrx1*nrx2*nrx3 IS NOT nrxx, but yet the charge density still > only has rho(1:nrxx) values, right? some time ago I answered "wrong" to some question on this mailing list, and Nicola - who knows English way better than me - told me that it gave a bad impression. So I am not going to do it again, but I should :-) On one processor, nrx1, nrx2, nrx3 are the physical dimensions of rho (and of all FFT arrays in real space). rho contains nrxx=nrx1*nrx2*nrx3 elements, but only rho(i,j,k) with i=1,...,nr1, j =1,..,nr2, k=1,...,nr3, correspond to "true" elements. The remaining ones have to be set to zero. Note that (i,j,k) => 1+(i-1)+(j-1)*nrx1+(k-1)*nrx1*nrx2 in fortran. Complicated? yes, and a frequent source of nasty errors. Unfortunately memory conflicts on some architectures are so serious that without this trick execution times for FFTs may double or triple. Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From chenhanghuipwscf at gmail.com Sat May 3 00:10:20 2008 From: chenhanghuipwscf at gmail.com (alan chen) Date: Fri, 2 May 2008 18:10:20 -0400 Subject: [Pw_forum] ultra-soft psedudo potential Message-ID: <22ae3ca40805021510j772e8ea2nc76c98b93d5d8034@mail.gmail.com> Dear PWSCF users, I know this might not be the right place to ask but I just want to give a try. I use the standard uspp-736 package to generate an ultra soft peseudo potential (downloaded from David's homepage). There is an option in the generation: "lloc" indicates which local potential to use. However if we set "lloc = -1", it means "simply match polynomial inside rcloc to ae potential outside" (from the menu). What does it really mean? Is there a local potential if we set "lloc = -1"? Thank you very much. Hanghui -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080502/f120bac3/attachment.htm From jgrz2010 at yahoo.com.mx Sat May 3 01:25:35 2008 From: jgrz2010 at yahoo.com.mx (JAIME GUSTAVO RODRIGUEZ ZAVALA) Date: Fri, 2 May 2008 18:25:35 -0500 (CDT) Subject: [Pw_forum] comparing gaussian03 with pwscf Message-ID: <747081.39575.qm@web34207.mail.mud.yahoo.com> Dear pwscf users, When analyzing the endohedral La at C60 molecule I obtain, using the gaussian03, a charge transfer from the La atom to the C60 cage, leaving the La atom with a charge of +2.12. However the pwscf charge calculation (with the La.pw91-nsp-van.UPF) gives also a charge transfer from the La atom to the C60 cage, but leaves the La atom with a charge of +1.08. Is this a natural difference between gaussian03 (natural population analysis) and pwscf (Lowdin analysis)? Thank you for the help you can provide. ____________________________________________________________________________________ Yahoo! Deportes Beta ?No te pierdas lo ?ltimo sobre el torneo clausura 2008! Ent?rate aqu? http://deportes.yahoo.com From yrehem at mac.com Sat May 3 01:35:42 2008 From: yrehem at mac.com (Yaser Rehem) Date: Fri, 02 May 2008 16:35:42 -0700 Subject: [Pw_forum] measuring covalent vs. ionic nature of Li bonding in LiC6 Message-ID: <87380A1E-91B1-4501-BE8B-2FBECF8B3B36@mac.com> Dear Pwscf Users- Can anyone offer advice on how best to measure the nature of Li bonding in LiC6? I've used projwfc.x to calculat the pDOS of the valence Li electron in a relaxed LiC6 structure, and I find the results surprising. If I use a gga ps, I find that the valence Li electron in LiC6 has an approximately 55% overlap with it's free valence states, and an approximately 69% overlap if I use an lda ps with a semi-core. Many studies show the charge transfer from Li to C in LiC6 to be almost complete--i.e., the Li is essentially fully ionized--hence my surprise at the pDOS results. Can anyone offer alternate method(s) by which I can assess the relative covalent vs. ionic nature of Li bonding in this structure? Thank you, -Yaser Rehem Rehem Research & Consulting (a.k.a. Yaser working in his basement :-) From paulatto at sissa.it Sat May 3 11:45:58 2008 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Sat, 3 May 2008 11:45:58 +0200 (CEST) Subject: [Pw_forum] ultra-soft psedudo potential In-Reply-To: <22ae3ca40805021510j772e8ea2nc76c98b93d5d8034@mail.gmail.com> References: <22ae3ca40805021510j772e8ea2nc76c98b93d5d8034@mail.gmail.com> Message-ID: <16416.82.56.168.93.1209807958.squirrel@webmail.sissa.it> On Sab, Maggio 3, 2008 00:10, alan chen wrote: > What does it really mean? Is there a > local potential if we set "lloc = -1"? Dear Hanghui, when generating the psedopotential you want to reproduce the scattering properties of the all-electron core with a local potential and some projectors functions. The projectors works at short radius, and compensate the inability of a simple local potential to produce the desired solutions for all energies and angular momenta. Usually you can choose one special angular momentum and a reference energy to be used as local channel; this has several implications: the local channel has to be norm-conserving, cannot have a second reference energy, cannot have ghost states. So usually you want to choose the higher possible L for the local channel to reduce the number of projectors (you have one for each M=-L,..,L). Instead you often wind up taking a lower L in order to remove a ghost state. The point is that it is not a must to use a local channel, actually as long as it matches the all-electron potential outside the pseudization region, you can take *any* function as a local potential. As a drawback you will have to use (at least) one projector for each value of L; this can make you pseudopotential slower or less transferable. Sometimes it is the only way to avoid the presence of ghost states. -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) +39 040 3787 511 http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From natalie at wfu.edu Sat May 3 17:55:39 2008 From: natalie at wfu.edu (Natalie Holzwarth) Date: Sat, 3 May 2008 11:55:39 -0400 (EDT) Subject: [Pw_forum] measuring covalent vs. ionic nature of Li bonding in LiC6 In-Reply-To: <87380A1E-91B1-4501-BE8B-2FBECF8B3B36@mac.com> References: <87380A1E-91B1-4501-BE8B-2FBECF8B3B36@mac.com> Message-ID: We studied LiC6 many years ago -- Phys. Rev. B 28, 1013 (1983) and there have been quite a few others who have studied it since. If I remember correctly, to a very rough approximation you can interpret the band structure results as Li donating its charge to the graphite pi bands. To complicate the picture, Posternak and co-workers Phys. Rev. Lett. 50, 761 - 764 (1983) pointed out an existence of an interlayer band which we later (Phys. Rev. B 30, 2219 (1984)) tried to reconcile with the Li donor band picture. However, what is the physical distribution of the charge in the vicinity of the Li site is another story. Within the picture of the top valence bands of LiC6 being primarily composed of C pi states, there will still be electron density near the Li site. To determine whether this electron density is due to a superposition of C pi states or whether there is some hybridization with Li 2s states is very difficult to determine quantitatively in the sense there is not an obvious way to partition the charge. As long as you are careful to report how you you do your analysis you will at least have a reproducible parameter.... That's my 2 cents worth. Natalie Holzwarth On Fri, 2 May 2008, Yaser Rehem wrote: > Dear Pwscf Users- > > Can anyone offer advice on how best to measure the nature of Li > bonding in LiC6? I've used projwfc.x to calculat the pDOS of the > valence Li electron in a relaxed LiC6 structure, and I find the > results surprising. If I use a gga ps, I find that the valence Li > electron in LiC6 has an approximately 55% overlap with it's free > valence states, and an approximately 69% overlap if I use an lda ps > with a semi-core. Many studies show the charge transfer from Li to C > in LiC6 to be almost complete--i.e., the Li is essentially fully > ionized--hence my surprise at the pDOS results. > > Can anyone offer alternate method(s) by which I can assess the > relative covalent vs. ionic nature of Li bonding in this structure? > > Thank you, > > -Yaser Rehem > Rehem Research & Consulting > (a.k.a. Yaser working in his basement :-) > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > N. A. W. Holzwarth email: natalie at wfu.edu Department of Physics www: http://www.wfu.edu/~natalie Wake Forest University voice: 336-758-5510 Winston-Salem, NC 27109-7507 fax: 336-758-6142 U. S. A. From baroni at sissa.it Sun May 4 22:03:01 2008 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 4 May 2008 22:03:01 +0200 Subject: [Pw_forum] [OT] How to identify NFE states ? In-Reply-To: References: <4908A727-2A77-4B86-BECE-253200A81949@sissa.it> Message-ID: sorry, but this time I do not understand what you mean ... S> On Apr 30, 2008, at 11:56 AM, lan haiping wrote: > Thank you ,Stefano! > I have misinterpreted the meaning of effective mass. > When we talk about NFE states, does it mean that such > E-K dispersion should be held between 2 symmetry points, like from X- > > Gamma ? > > On Mon, Apr 28, 2008 at 1:40 AM, Stefano Baroni > wrote: > The higher the energy, the lower the effect of the pseudopotential, > so high-energy states are expected to be more free-electron like > than low-lying ones. I am afraid that the very ocncept of "effective > mass" is not very meaningful for these states. However, I would > expect (although I have never verified) that for high-lying states > the derivative of the band energy with respect to the wavenumber be > linear with respect to the wavenumber, with the coefficient given by > the inverse of the free-electron mass. SB > > On Apr 27, 2008, at 8:27 AM, lan haiping wrote: > >> Dear All, >> >> I am wondering about the nearly free electron states . To identify >> such states, >> does it mean that its effective mass is very close to free >> electron ,And we can identify >> it from bands' dispersion ? >> >> Bests >> H.P >> >> -- >> Hai-Ping Lan >> Department of Electronics , >> Peking University , Bejing, 100871 >> lanhaiping at gmail.com, hplan at pku.edu.cn >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - > Trieste > [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une > morale de la pens?e - Jean Piaget > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > Hai-Ping Lan > Department of Electronics , > Peking University , Bejing, 100871 > lanhaiping at gmail.com, hplan at pku.edu.cn > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080504/a21b10c1/attachment.htm From lanhaiping at gmail.com Mon May 5 01:21:01 2008 From: lanhaiping at gmail.com (lan haiping) Date: Mon, 5 May 2008 07:21:01 +0800 Subject: [Pw_forum] [OT] How to identify NFE states ? In-Reply-To: References: <4908A727-2A77-4B86-BECE-253200A81949@sissa.it> Message-ID: :(, i think i have misunderstood the states' identification. I thought we could just figure out states like NFEs from bands structure, and NFEs should have a similar energy dispersion of free electron between different high symmetry points. Of course, we should also take the fold-up into account for different BZs. After digging out some papers, i find we should judge state not just from bands calculation, but also consider the shape of wavefunction. I am really sorry for my poor expression and some misunderstangding, Thanks for your kindly reply and help. Best On Mon, May 5, 2008 at 4:03 AM, Stefano Baroni wrote: > sorry, but this time I do not understand what you mean ...S> > > On Apr 30, 2008, at 11:56 AM, lan haiping wrote: > > Thank you ,Stefano! > I have misinterpreted the meaning of effective mass. > When we talk about NFE states, does it mean that such > E-K dispersion should be held between 2 symmetry points, like from X-> > Gamma ? > > On Mon, Apr 28, 2008 at 1:40 AM, Stefano Baroni wrote: > > > The higher the energy, the lower the effect of the pseudopotential, so > > high-energy states are expected to be more free-electron like than low-lying > > ones. I am afraid that the very ocncept of "effective mass" is not very > > meaningful for these states. However, I would expect (although I have never > > verified) that for high-lying states the derivative of the band energy with > > respect to the wavenumber be linear with respect to the wavenumber, with the > > coefficient given by the inverse of the free-electron mass. SB > > On Apr 27, 2008, at 8:27 AM, lan haiping wrote: > > > > Dear All, > > > > I am wondering about the nearly free electron states . To identify such > > states, > > does it mean that its effective mass is very close to free electron ,And > > we can identify > > it from bands' dispersion ? > > > > Bests > > H.P > > > > -- > > Hai-Ping Lan > > Department of Electronics , > > Peking University , Bejing, 100871 > > lanhaiping at gmail.com, hplan at pku.edu.cn_______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > > --- > > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - > > Trieste > > [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) > > > > La morale est une logique de l'action comme la logique est une morale de > > la pens?e - Jean Piaget > > > > Please, if possible, don't send me MS Word or PowerPoint attachments > > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > -- > Hai-Ping Lan > Department of Electronics , > Peking University , Bejing, 100871 > lanhaiping at gmail.com, hplan at pku.edu.cn_______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste > [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une morale de > la pens?e - Jean Piaget > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080505/7004ba40/attachment-0001.htm From giannozz at nest.sns.it Mon May 5 20:59:34 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 5 May 2008 20:59:34 +0200 Subject: [Pw_forum] comparing gaussian03 with pwscf In-Reply-To: <747081.39575.qm@web34207.mail.mud.yahoo.com> References: <747081.39575.qm@web34207.mail.mud.yahoo.com> Message-ID: <4D1F432A-2806-4AA8-8E1B-29CDAAAE1BB8@nest.sns.it> On May 3, 2008, at 1:25 , JAIME GUSTAVO RODRIGUEZ ZAVALA wrote: > When analyzing the endohedral La at C60 molecule I > obtain, using the gaussian03, a charge transfer from > the La atom to the C60 cage, leaving the La atom with > a charge of +2.12. However the pwscf charge > calculation (with the La.pw91-nsp-van.UPF) gives also > a charge transfer from the La atom to the C60 cage, > but leaves the La atom with a charge of +1.08. Is this > a natural difference between gaussian03 (natural > population analysis) and pwscf (Lowdin analysis)? hard to say. How well do electronic structures with gaussian and with plane waves compare? if they are similar, maybe the difference is in the different procedure to assign charges to atoms. 1 electron difference look large, though. Maybe one should see what happens is simpler systems. Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From baris.malcioglu at gmail.com Mon May 5 20:25:39 2008 From: baris.malcioglu at gmail.com (O. Baris Malcioglu) Date: Mon, 05 May 2008 21:25:39 +0300 Subject: [Pw_forum] comparing gaussian03 with pwscf In-Reply-To: <4D1F432A-2806-4AA8-8E1B-29CDAAAE1BB8@nest.sns.it> References: <747081.39575.qm@web34207.mail.mud.yahoo.com> <4D1F432A-2806-4AA8-8E1B-29CDAAAE1BB8@nest.sns.it> Message-ID: <481F5123.7070300@gmail.com> Hi, Maybe some details on how you are calculating the system in Gaussian will be helpful, especially the basis set and the X-C functionals. I suspect the problem arises from the intrinsic difficulty of describing Carbon atoms and Lanthanium at the same time using all-electron wavefunctions. You should pay extra attention how your carbon cores are described in a set that is tailored for Lanthanoids, or vice versa. O. Baris Malcioglu SISSA CM sector, Trieste, Italy Tel:+390403787374 > On May 3, 2008, at 1:25 , JAIME GUSTAVO RODRIGUEZ ZAVALA wrote: > > >> When analyzing the endohedral La at C60 molecule I >> obtain, using the gaussian03, a charge transfer from >> the La atom to the C60 cage, leaving the La atom with >> a charge of +2.12. However the pwscf charge >> calculation (with the La.pw91-nsp-van.UPF) gives also >> a charge transfer from the La atom to the C60 cage, >> but leaves the La atom with a charge of +1.08. Is this >> a natural difference between gaussian03 (natural >> population analysis) and pwscf (Lowdin analysis)? >> From akohlmey at cmm.chem.upenn.edu Mon May 5 21:25:18 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Mon, 5 May 2008 15:25:18 -0400 (EDT) Subject: [Pw_forum] comparing gaussian03 with pwscf In-Reply-To: <481F5123.7070300@gmail.com> References: <747081.39575.qm@web34207.mail.mud.yahoo.com> <4D1F432A-2806-4AA8-8E1B-29CDAAAE1BB8@nest.sns.it> <481F5123.7070300@gmail.com> Message-ID: On Mon, 5 May 2008, O. Baris Malcioglu wrote: BM> Hi, BM> BM> Maybe some details on how you are calculating the system in Gaussian BM> will be helpful, especially the basis set and the X-C functionals. I BM> suspect the problem arises from the intrinsic difficulty of describing BM> Carbon atoms and Lanthanium at the same time using all-electron BM> wavefunctions. You should pay extra attention how your carbon cores are BM> described in a set that is tailored for Lanthanoids, or vice versa. baris, i beg to differ. there may be basis set completenes issues when using a too small basis set, but why should you need to tailor the carbon basis set for lanthanoids? the whole point of having defined basis sets is, that those _are_ balanced. so that should at most be a minor effect. i would rather expect the differences arising from much more obvious issues. i.e., a) the fact that you have to project your plane wave wavefunction on an atomic basis set and that this projection cannot be complete, since you don't have a complete basis set that you project on. rather you use a minimal basis built from the atomic pseudowavefunctions. you can easily lose 1-2 electrons here. b) as paolo already noted, the differences between different ways to perform the population analysis. e.g. mulliken vs. loewdin vs. nbo vs. ... if you have access to the CPMD (www.cpmd.org) code you can easily see how large those effects can be, as the code allows to project on either atomic pseudo wavefunction or a minimal slater basis (or any gaussian basis you define in the input) as well as it supports mulliken and loewdin like analysis. comparing the dependence of the thusly calculated partial charges from plane waves on the basis set and method is quite educational... (not to mention the impact of pseudopotentials, plane wave cutoff etc...). we are frequently tempted to put too much trust into the many digits of numbers that we calculate. their absolute accuracy can be _much_ less. cheers, axel. BM> BM> O. Baris Malcioglu BM> SISSA CM sector, BM> Trieste, Italy BM> Tel:+390403787374 BM> BM> > On May 3, 2008, at 1:25 , JAIME GUSTAVO RODRIGUEZ ZAVALA wrote: BM> > BM> > BM> >> When analyzing the endohedral La at C60 molecule I BM> >> obtain, using the gaussian03, a charge transfer from BM> >> the La atom to the C60 cage, leaving the La atom with BM> >> a charge of +2.12. However the pwscf charge BM> >> calculation (with the La.pw91-nsp-van.UPF) gives also BM> >> a charge transfer from the La atom to the C60 cage, BM> >> but leaves the La atom with a charge of +1.08. Is this BM> >> a natural difference between gaussian03 (natural BM> >> population analysis) and pwscf (Lowdin analysis)? BM> >> BM> _______________________________________________ BM> Pw_forum mailing list BM> Pw_forum at pwscf.org BM> http://www.democritos.it/mailman/listinfo/pw_forum BM> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From baris.malcioglu at gmail.com Mon May 5 22:12:09 2008 From: baris.malcioglu at gmail.com (O. Baris Malcioglu) Date: Mon, 05 May 2008 23:12:09 +0300 Subject: [Pw_forum] comparing gaussian03 with pwscf In-Reply-To: References: <747081.39575.qm@web34207.mail.mud.yahoo.com> <4D1F432A-2806-4AA8-8E1B-29CDAAAE1BB8@nest.sns.it> <481F5123.7070300@gmail.com> Message-ID: <481F6A19.2010503@gmail.com> I completely agree with you, but I think what I have in mind is much more trivial than that. When calculating a system in Gaussian using AE wavefunctions you are to find a basis set that describes all atoms in the structure simultaneously, unless you are using something like an ONIOM model, which has added complications. For example, when using PWSCF, you can use La.pbe-nsp-van.UPF for the Lanthanide and say C.pbe-van_ak.UPF for the carbon, and since the valance set will consist of (different combination of) planewaves on -both- sides, the both PPs are interoperable. On the contrary, using something like 6-31G* for the Carbon and LanL2DZ for the Lanthanide is not possible straightforwardly in a Gaussian AE calculation since the very definition of valance basis functions are different on these sets. Looking at the corresponding manual at http://www.gaussian.com/g_ur/m_basis_sets.htm you can see that for a basis set that describes both La and C simultaneously, the choices are quite limited, and coarse if used straightforwardly. Thus, I think there might be a chance that the charge difference is arising from having forced to use too coarse basis sets. Well, I hope another view on the matter helps. O. Baris Malcioglu SISSA CM sector, Trieste, Italy Axel Kohlmeyer wrote: > i beg to differ. there may be basis set completenes issues when > using a too small basis set, but why should you need to tailor > the carbon basis set for lanthanoids? the whole point of having > defined basis sets is, that those _are_ balanced. so that should > at most be a minor effect. > > i would rather expect the differences arising from much > more obvious issues. i.e., > > a) the fact that you have to project your plane wave wavefunction > on an atomic basis set and that this projection cannot be > complete, since you don't have a complete basis set that > you project on. rather you use a minimal basis built from the > atomic pseudowavefunctions. you can easily lose 1-2 electrons here. > > b) as paolo already noted, the differences between different ways > to perform the population analysis. e.g. mulliken vs. loewdin vs. > nbo vs. ... > > if you have access to the CPMD (www.cpmd.org) code you can easily see > how large those effects can be, as the code allows to project on > either atomic pseudo wavefunction or a minimal slater basis (or any > gaussian basis you define in the input) as well as it supports mulliken > and loewdin like analysis. comparing the dependence of the thusly > calculated partial charges from plane waves on the basis set and > method is quite educational... (not to mention the > impact of pseudopotentials, plane wave cutoff etc...). > > we are frequently tempted to put too much trust into the many > digits of numbers that we calculate. their absolute accuracy > can be _much_ less. > > cheers, > axel. From wjyin at fudan.edu.cn Tue May 6 05:19:19 2008 From: wjyin at fudan.edu.cn (yinwanjian) Date: Tue, 06 May 2008 11:19:19 +0800 Subject: [Pw_forum] Question on Makov-Payne corrections Message-ID: Dear QE users, I am calculating the charged isolated clusters and find that PWSCF deal with negative charged system by adding an homogenous positive charge background and using Makov-Payne corrections [Phy. Rev. B 51, 4014 (1995)]. As described in above reference, Mokov-Payne method calculated the total energy of negative charged cluster and uniform positive background as E_0, and divide the total charge density into two neutral part, the electrosta ic energy of one of which is Madelung energy E_11, and the interaction energy of two neutral part is E_12. Then Mokov-Payne consider the expected energy of negative cluster as E = E_22 = E_0 - E_11 - E_12. However, I don't think E is the energy of negative cluster but of the negative cluster plus one positive point charge, which is a neutral system. I am looking forward to your replies. Thanks. best Yin Wanjian Ph.D Candidates Department of Physics, Fudan University Shanghai, China From Mohamed.Majdoub at mail.uh.edu Tue May 6 06:32:21 2008 From: Mohamed.Majdoub at mail.uh.edu (Mohamed.Majdoub at mail.uh.edu) Date: Mon, 05 May 2008 23:32:21 -0500 Subject: [Pw_forum] metal insulator interface simulation! Message-ID: Dear users, I am a new user of Pwscf. I need to study the polarization, dielectric constant, local electrostatic potential.. of Au/MgO (100) interface. First, we need a relaxation/structural optimization calculation to find out the optimal interface configuration. Then I need to extract the local potential at different positions from the interface. The issues I am facing are: 1- how can I combine a metal and insulator in the same calculation and input file? I know that for metal we need to specify how metallicity is treated (occupations='smearing' for example). If I specify it in the same input file will it be fine for the insulator. 2- how can I extract local potential? In the manual pp.x (post processing) we have plot_num??? selects what is saved in filplot: ? !??????????????? 1=total potential V_bare+V_H + V_xc ? !??????????????? 2=local ionic potential ? !?????????????? 11=the V_bare + V_H potential ? !?????????????? 12=the electric field potential which of these quantity will correspond to the total local potential (ionic + Hartree)? exact definition for Hartree and exchange correlation contributions? Please advice if you have any useful information that can help me out. Your suggestions and help are welcomed! Thank you in advance! Mohamed Sabri Majdoub PhD candidate Mechanical Engineering University of Houston USA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080505/3137690d/attachment.htm From eariel99 at gmail.com Tue May 6 21:06:12 2008 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Tue, 6 May 2008 15:06:12 -0400 Subject: [Pw_forum] openmp vs mpich performance with MKL 10.x Message-ID: Hi, I have noted recently that I am able to obtain faster binaries of pw.x using the the OpenMP paralellism implemented in the Intel MKL libraries of version 10.xxx, than using MPICH, in the Intel cpus. Previously I had always gotten better performance using MPI. I would like to know of other experience on how to make the machines faster. Let me explain in more details. Compiling using MPI means using mpif90 as linker and compiler, linking against mkl_ia32 or mkl_em64t, and using link flags -i-static -openmp. This is just the what appears in the make.sys after running configure in version 4cvs, At runtime, I set export OMP_NUM_THREADS=1 export MKL_NUM_THREADS=1 and run using mpiexec -n $NCPUs pw.x output where NCPUs is the number of cores available in the system. The second choice is ./configure --disable-parallel and at runtime export OMP_NUM_THREADS=$NCPU export MKL_NUM_THREADS=$NCPU and run using pw.x output I have tested it in Quadcores (NCPU=4) and with an old Dual Xeon B.C. (before cores) (NCPU=2). Before April 2007, the first choice had always workes faster. After that, when I came to use the MKL 10.xxx, the second choice is working faster. I have found no significant difference between version 3.2.3 and 4cvs. A special comment is for the FFT library. The MKL has a wrapper to the FFTW, that must be compiled after instalation (it is very easy). This creates additional libraries named like libfftw3xf_intel.a and libfftw2xf_intel.a This allows improves the performance in the second choice, specially with libfftw3xf_intel.a. Using MPI, libfftw2xf_intel.a is as fast as using the FFTW source distributed with espresso, i.e., there is no gain in using libfftw2xf_intel.a. With libfftw3xf_intel.a and MPI, I have never been able to run pw.x succesfully, it just aborts. I would like to hear of your experiences. Best regards Eduardo Menendez University of Chile -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080506/ca00a740/attachment.htm From akohlmey at cmm.chem.upenn.edu Tue May 6 20:51:51 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 6 May 2008 14:51:51 -0400 (EDT) Subject: [Pw_forum] openmp vs mpich performance with MKL 10.x In-Reply-To: References: Message-ID: On Tue, 6 May 2008, Eduardo Ariel Menendez Proupin wrote: EAMP> Hi, EAMP> I have noted recently that I am able to obtain faster binaries of pw.x using EAMP> the the OpenMP paralellism implemented in the Intel MKL libraries of version EAMP> 10.xxx, than using MPICH, in the Intel cpus. Previously I had always gotten EAMP> better performance using MPI. I would like to know of other experience on EAMP> how to make the machines faster. Let me explain in more details. EAMP> EAMP> Compiling using MPI means using mpif90 as linker and compiler, linking EAMP> against mkl_ia32 or mkl_em64t, and using link flags -i-static -openmp. This EAMP> is just the what appears in the make.sys after running configure in version EAMP> 4cvs, EAMP> EAMP> At runtime, I set EAMP> export OMP_NUM_THREADS=1 EAMP> export MKL_NUM_THREADS=1 EAMP> and run using EAMP> mpiexec -n $NCPUs pw.x output EAMP> where NCPUs is the number of cores available in the system. EAMP> EAMP> The second choice is EAMP> ./configure --disable-parallel EAMP> EAMP> and at runtime EAMP> export OMP_NUM_THREADS=$NCPU EAMP> export MKL_NUM_THREADS=$NCPU EAMP> and run using EAMP> pw.x output EAMP> EAMP> I have tested it in Quadcores (NCPU=4) and with an old Dual Xeon B.C. EAMP> (before cores) (NCPU=2). EAMP> EAMP> Before April 2007, the first choice had always workes faster. After that, EAMP> when I came to use the MKL 10.xxx, the second choice is working faster. I EAMP> have found no significant difference between version 3.2.3 and 4cvs. EAMP> EAMP> A special comment is for the FFT library. The MKL has a wrapper to the FFTW, EAMP> that must be compiled after instalation (it is very easy). This creates EAMP> additional libraries named like libfftw3xf_intel.a and libfftw2xf_intel.a EAMP> This allows improves the performance in the second choice, specially with EAMP> libfftw3xf_intel.a. EAMP> EAMP> Using MPI, libfftw2xf_intel.a is as fast as using the FFTW source EAMP> distributed with espresso, i.e., there is no gain in using EAMP> libfftw2xf_intel.a. With libfftw3xf_intel.a and MPI, I have never been able EAMP> to run pw.x succesfully, it just aborts. EAMP> EAMP> I would like to hear of your experiences. eduardo, there are two issue that need to be considered. 1) how large are your test jobs? if they are not large enough, timings are pointless. 2) it is most likely, that you are still tricked by the auto-parallelization of intel MKL. the export OMP_NUM_THREADS will usually only work for the _local_ copy, for some MPI startup mechanisms not at all. thus your MPI jobs will be slowed down. to make certain that you only like the serial version of MKL with your MPI executable, please replace -lmkl_em64t in your make.sys file with -lmkl_intel_lp64 -lmkl_sequential -lmkl_core you may have to add: -Wl,-rpath,/opt/intel/path/to/your/mkl to make your executable find the libraries at runtime. with those executable you can try again, and i would be _very_ surprised if using MPI is slower than serial and multi-threading. i made tests with intel FFT vs. FFTW in a number of plane wave codes and the intel FFT was always slower. cheers, axel. EAMP> EAMP> Best regards EAMP> Eduardo Menendez EAMP> University of Chile EAMP> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From marzari at MIT.EDU Tue May 6 21:21:49 2008 From: marzari at MIT.EDU (Nicola Marzari) Date: Tue, 06 May 2008 15:21:49 -0400 Subject: [Pw_forum] openmp vs mpich performance with MKL 10.x In-Reply-To: References: Message-ID: <4820AFCD.70608@mit.edu> Dear Eduardo, our own experiences are summarized here: http://quasiamore.mit.edu/pmwiki/index.php?n=Main.CP90Timings It would be great if you could contribute your own data, either for pw.x or cp.x under the conditions you describe. I noticed indeed, informally, a few of the things you mention: 1) no improvements with the Intel fftw2 wrapper, as opposed to fftw2 Q-E sources, when using mpi. I also never managed to successfully run with the Intel fftw3 wrapper (or with fftw3 - that probably says something about me). 2) great improvements of a serial code (different from Q-E) when using the automatic parallelism of MKL in quad-cores. 3) btw, MPICH has always been for us the slower protocol, compared with LAMMPI or OpenMPI I actually wonder if the best solution on a quad-core would be, say, to use two cores for MPI, and the other two for the openmp threads. I eagerly await Axel's opinion. nicola Eduardo Ariel Menendez Proupin wrote: > Hi, > I have noted recently that I am able to obtain faster binaries of pw.x > using the the OpenMP paralellism implemented in the Intel MKL libraries > of version 10.xxx, than using MPICH, in the Intel cpus. Previously I had > always gotten better performance using MPI. I would like to know of > other experience on how to make the machines faster. Let me explain in > more details. > > Compiling using MPI means using mpif90 as linker and compiler, linking > against mkl_ia32 or mkl_em64t, and using link flags -i-static -openmp. > This is just the what appears in the make.sys after running configure > in version 4cvs, > > At runtime, I set > export OMP_NUM_THREADS=1 > export MKL_NUM_THREADS=1 > and run using > mpiexec -n $NCPUs pw.x output > where NCPUs is the number of cores available in the system. > > The second choice is > ./configure --disable-parallel > > and at runtime > export OMP_NUM_THREADS=$NCPU > export MKL_NUM_THREADS=$NCPU > and run using > pw.x output > > I have tested it in Quadcores (NCPU=4) and with an old Dual Xeon B.C. > (before cores) (NCPU=2). > > Before April 2007, the first choice had always workes faster. After > that, when I came to use the MKL 10.xxx, the second choice is working > faster. I have found no significant difference between version 3.2.3 and > 4cvs. > > A special comment is for the FFT library. The MKL has a wrapper to the > FFTW, that must be compiled after instalation (it is very easy). This > creates additional libraries named like libfftw3xf_intel.a and > libfftw2xf_intel.a > This allows improves the performance in the second choice, specially > with libfftw3xf_intel.a. > > Using MPI, libfftw2xf_intel.a is as fast as using the FFTW source > distributed with espresso, i.e., there is no gain in using > libfftw2xf_intel.a. With libfftw3xf_intel.a and MPI, I have never been > able to run pw.x succesfully, it just aborts. > > I would like to hear of your experiences. > > Best regards > Eduardo Menendez > University of Chile > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From eariel99 at gmail.com Tue May 6 21:22:53 2008 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Tue, 6 May 2008 15:22:53 -0400 Subject: [Pw_forum] comparing gaussian03 with pwscf Message-ID: If there is doubt on the approximations for lantanides, I suggest to make some tests with something more "classic", such as NaCl or MgO and then compare PWSCF vs GAUSSIAN with complete basis sets. One question? What is the useful information provided by the knowledge of the charge transfer? Can it be correlated to any measurable property (reactivity, entropy, adsorcion enrgy, ....) or with any measurable and difficult to calculate property? Some years ago I calculated and reported some charge transfer and said something about the ionicity. To know better, I calculated the charge transfer in NaCl. For this, I integrated the charge density in the Voronoi cells of Na and Cl, using the self consisten charge density and the superposition of atomic densities. The difference is the charge transfer or, more precisely, the charge that crosses the boundary of the Voronoi cells. To my surprise, the charge transfer in NaCl is 0.1 electron, and not 1 electron as the textbooks suggest. I also tested it with MgO (0.2 instead of 2). So, where is hidden the truth of the ionic bond? -- Eduardo Menendez -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080506/bac4d315/attachment.htm From marzari at MIT.EDU Tue May 6 21:35:05 2008 From: marzari at MIT.EDU (Nicola Marzari) Date: Tue, 06 May 2008 15:35:05 -0400 Subject: [Pw_forum] measuring covalent vs. ionic nature of Li bonding in LiC6 In-Reply-To: <87380A1E-91B1-4501-BE8B-2FBECF8B3B36@mac.com> References: <87380A1E-91B1-4501-BE8B-2FBECF8B3B36@mac.com> Message-ID: <4820B2E9.4060906@mit.edu> Yaser Rehem wrote: > Can anyone offer alternate method(s) by which I can assess the > relative covalent vs. ionic nature of Li bonding in this structure? Dear Yaser, one measure that I like is the Born effective charge - it's a real physical quantity, and it tells you how an atom responds to an electric field. If the bonding is ionic, the atom will respond exactly as you expect from its formal charge - if covalent it will be different. This topic has been often discussed in the ferroelectrics literature, due to the interested in the origin for the "giant" effective charges of O. You could also look at a recent PRB by Abdallah Qteish (Phys. Rev. B 75, 085201 (2007)) on ionicity. nicola --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From marzari at MIT.EDU Tue May 6 21:37:44 2008 From: marzari at MIT.EDU (Nicola Marzari) Date: Tue, 06 May 2008 15:37:44 -0400 Subject: [Pw_forum] Question on Makov-Payne corrections In-Reply-To: References: Message-ID: <4820B388.2020603@mit.edu> yinwanjian wrote: > I am looking forward to your replies. Thanks. PHYSICAL REVIEW B 77, 115139 (2008). -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From marzari at MIT.EDU Tue May 6 21:43:30 2008 From: marzari at MIT.EDU (Nicola Marzari) Date: Tue, 06 May 2008 15:43:30 -0400 Subject: [Pw_forum] metal insulator interface simulation! In-Reply-To: References: Message-ID: <4820B4E2.6050208@mit.edu> Mohamed.Majdoub at mail.uh.edu wrote: > 1- how can I combine a metal and insulator in the same calculation and > input file? > I know that for metal we need to specify how metallicity is treated > (occupations='smearing' for example). If I specify it in the same input > file will it be fine for the insulator. Yes, treat everything as a metal. Even if you were to treat a "pure" insulator as a metal, you'd discover that, provided the gap is larger (a few times) than the smearing temperature, the unoccupied bands are empty, and your calculations reproduce the same results you'd obtain by treating the insulator as an insulator. > 2- how can I extract local potential? > In the manual pp.x (post processing) we have > > plot_num selects what is saved in filplot: > > ! 1=total potential V_bare+V_H + V_xc > ! 2=local ionic potential > ! 11=the V_bare + V_H potential > ! 12=the electric field potential > > which of these quantity will correspond to the total local potential > (ionic + Hartree)? > exact definition for Hartree and exchange correlation contributions? > > Please advice if you have any useful information that can help me out. > Your suggestions and help are welcomed! Have a careful look at Caspar Fall PhD thesis, from www.epfl.ch . Look at the recent papers by Stengel and Spaldin (Nature, and PRB). Try and see how 1, 2, and 11 look like. nicola -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From eariel99 at gmail.com Tue May 6 21:44:03 2008 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Tue, 6 May 2008 15:44:03 -0400 Subject: [Pw_forum] openmp vs mpich performance with MKL 10.x In-Reply-To: References: Message-ID: > there are two issue that need to be considered. > > 1) how large are your test jobs? if they are not large enough, timings are > pointless. about 15 minutes in Intel Quadcore. 66 atoms: Cd_30Te_30O_6. 576 electrons in total. My test may be very particular. If you a have a balanced benchmark, I would like to run it. > 2) it is most likely, that you are still tricked by the > auto-parallelization of intel MKL. the export OMP_NUM_THREADS > will usually only work for the _local_ copy, for some > MPI startup mechanisms not at all. thus your MPI jobs will > be slowed down. I am using only SMP. Sorry, I still haven't a cluster of Quadcores. > > > to make certain that you only like the serial version of > MKL with your MPI executable, please replace -lmkl_em64t > in your make.sys file with > -lmkl_intel_lp64 -lmkl_sequential -lmkl_core Yes, I also tried that. The test runs in 14m2s. Using only -lmkl_em64t it runs in 14m31s. Using serial compilations it ran in 12m20s. Thanks, Eduardo -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080506/ef1744f2/attachment.htm From akohlmey at cmm.chem.upenn.edu Tue May 6 21:27:24 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 6 May 2008 15:27:24 -0400 (EDT) Subject: [Pw_forum] openmp vs mpich performance with MKL 10.x In-Reply-To: <4820AFCD.70608@mit.edu> References: <4820AFCD.70608@mit.edu> Message-ID: On Tue, 6 May 2008, Nicola Marzari wrote: NM> NM> Dear Eduardo, hi nicola, NM> 1) no improvements with the Intel fftw2 wrapper, as opposed to fftw2 NM> Q-E sources, when using mpi. I also never managed to successfully run NM> with the Intel fftw3 wrapper (or with fftw3 - that probably says NM> something about me). no it doesn't. i NM> 2) great improvements of a serial code (different from Q-E) when using NM> the automatic parallelism of MKL in quad-cores. nod. i just yesterday made some tests with different BLAS/LAPACK implementations, and it turns out that the 10.0 MKL is pretty effecient in parallelizing tasks like DGEMM. through use of SSE2/3/4 and multi threading you can get easily a factor of 6 improvement on a 4-core node. NM> NM> 3) btw, MPICH has always been for us the slower protocol, compared with NM> LAMMPI or OpenMPI NM> NM> I actually wonder if the best solution on a quad-core would be, say, NM> to use two cores for MPI, and the other two for the openmp threads. this is a _very_ tricky issue. usually for a plane wave pseudopotential codes, that distributed data parallelization is pretty efficient, except for the 3d-fourier transforms across the whole data set, which are very sensitive to network latencies. for jobs using k-points, you also have the option to parallelize over k-points with is very efficient, even on not so fast networks. with the CVS versions, you have another level of parallelism added (parallelisation over function instead of data = task groups). thus given an ideal network, you first want to exploit MPI parallelism maximally and then what is left is rather small, and - sadly - OpenMP doesn't work very efficiently on that. the overhead of spawning, synchronizing and joining threads is too high compared to the gain through parallelism. but we live in a real world and there are unexpected side effects and non-ideal machines and networks. e.g. when using nodes with many cores, e.g. two-socket quad-core, you have to "squeeze" a lot of communication through just one network card (be it infiniband, myrinet or ethernet) that will serialize communication and add unwanted conflicts and latencies. i've seen this happen particularly when using a very large number of nodes where you can run out of (physical) memory simply because of the way how the lowlevel communication was programmed. in that case you may indeed be better off using only half or a quarter of the cores with MPI and then set OMP_NUM_THREADS to 2 or even keep it at 1 (because that will, provided you have an MPI with processor affinity and optimal job placement, double the cpu cache). it is particularly interesting to discuss from this perspective having multi-core nodes connected by a high-latency TCP/IP network (e.g. gigabit ethernet). here with one MPI task per node you reach the limit of scaling pretty fast, and also using multiple MPI tasks per node is mostly multiplying the latencies, which is not helping. under those circumstance the data set is still rather large and then OpenMP parallelism can help to get the most out of a given machine. as noted before, it would be _even_ better if OpenMP directives were added to time critical and multi-threadable parts of QE. i have experienced this in CPMD where i managed to get about 80% of the MPI performance with the latest (extensively threaded) development sources and a fully-multi-threaded toolchain on a single node. however, running across multiple nodes quickly reduces the effectivity of the OpenMP support. just with two nodes you are at 60% only. now, deciding on what is the best combination of options is a very tricky multi-dimensional optimization problem you have to consider the following: - the size of the typical problem and job type - whether you can benefit from k-point parallelism - whether you prefer faster execution over cost efficiency and throughput. - the total amount of money you want to spend - the skillset of people that have to run the machine - how many people have to share the machine. - how I/O bound the jobs are. - how much memory you need and how much money you are willing to invest in faster memory. - failure rates and the level of service (gigabit equipment is easily available). also some of those parameters are (non-linearly) coupled which makes the decision making process even nastier. cheers, axel. NM> NM> I eagerly await Axel's opinion. NM> NM> nicola NM> NM> Eduardo Ariel Menendez Proupin wrote: NM> > Hi, NM> > I have noted recently that I am able to obtain faster binaries of pw.x NM> > using the the OpenMP paralellism implemented in the Intel MKL libraries NM> > of version 10.xxx, than using MPICH, in the Intel cpus. Previously I had NM> > always gotten better performance using MPI. I would like to know of NM> > other experience on how to make the machines faster. Let me explain in NM> > more details. NM> > NM> > Compiling using MPI means using mpif90 as linker and compiler, linking NM> > against mkl_ia32 or mkl_em64t, and using link flags -i-static -openmp. NM> > This is just the what appears in the make.sys after running configure NM> > in version 4cvs, NM> > NM> > At runtime, I set NM> > export OMP_NUM_THREADS=1 NM> > export MKL_NUM_THREADS=1 NM> > and run using NM> > mpiexec -n $NCPUs pw.x output NM> > where NCPUs is the number of cores available in the system. NM> > NM> > The second choice is NM> > ./configure --disable-parallel NM> > NM> > and at runtime NM> > export OMP_NUM_THREADS=$NCPU NM> > export MKL_NUM_THREADS=$NCPU NM> > and run using NM> > pw.x output NM> > NM> > I have tested it in Quadcores (NCPU=4) and with an old Dual Xeon B.C. NM> > (before cores) (NCPU=2). NM> > NM> > Before April 2007, the first choice had always workes faster. After NM> > that, when I came to use the MKL 10.xxx, the second choice is working NM> > faster. I have found no significant difference between version 3.2.3 and NM> > 4cvs. NM> > NM> > A special comment is for the FFT library. The MKL has a wrapper to the NM> > FFTW, that must be compiled after instalation (it is very easy). This NM> > creates additional libraries named like libfftw3xf_intel.a and NM> > libfftw2xf_intel.a NM> > This allows improves the performance in the second choice, specially NM> > with libfftw3xf_intel.a. NM> > NM> > Using MPI, libfftw2xf_intel.a is as fast as using the FFTW source NM> > distributed with espresso, i.e., there is no gain in using NM> > libfftw2xf_intel.a. With libfftw3xf_intel.a and MPI, I have never been NM> > able to run pw.x succesfully, it just aborts. NM> > NM> > I would like to hear of your experiences. NM> > NM> > Best regards NM> > Eduardo Menendez NM> > University of Chile NM> > NM> > NM> > ------------------------------------------------------------------------ NM> > NM> > _______________________________________________ NM> > Pw_forum mailing list NM> > Pw_forum at pwscf.org NM> > http://www.democritos.it/mailman/listinfo/pw_forum NM> NM> NM> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From akohlmey at cmm.chem.upenn.edu Tue May 6 21:39:52 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 6 May 2008 15:39:52 -0400 (EDT) Subject: [Pw_forum] openmp vs mpich performance with MKL 10.x In-Reply-To: References: Message-ID: On Tue, 6 May 2008, Eduardo Ariel Menendez Proupin wrote: EAMP> > there are two issue that need to be considered. EAMP> > EAMP> > 1) how large are your test jobs? if they are not large enough, timings are EAMP> > pointless. EAMP> about 15 minutes in Intel Quadcore. 66 atoms: Cd_30Te_30O_6. 576 EAMP> electrons in total. My test may be very particular. If you a have hmmm... that is pretty large. would you mind sending me the input. i'd like to make some verifications on my machine (two-socket dual core). EAMP> a balanced benchmark, I would like to run it. i've only done these kind of benchmarks systematically with CPMD, and only a few confirmation tests with QE. in general the G-space parallelization is comparable. while the individual performance for a specific problem can be quite different (QE is far superior with ultra-soft and k-points, CPMD outruns cp.x with norm-conserving pseudos), the scaling behavior was always quite similar for small to medium numbers of nodes. EAMP> > 2) it is most likely, that you are still tricked by the EAMP> > auto-parallelization of intel MKL. the export OMP_NUM_THREADS EAMP> > will usually only work for the _local_ copy, for some EAMP> > MPI startup mechanisms not at all. thus your MPI jobs will EAMP> > be slowed down. EAMP> EAMP> I am using only SMP. Sorry, I still haven't a cluster of Quadcores. that still does not mean that the environment is exported. some MPICH versions have pretty awkward ways of starting MPI environments that do not always forward the environment at all. EAMP> > to make certain that you only like the serial version of EAMP> > MKL with your MPI executable, please replace -lmkl_em64t EAMP> > in your make.sys file with EAMP> > -lmkl_intel_lp64 -lmkl_sequential -lmkl_core EAMP> EAMP> EAMP> Yes, I also tried that. The test runs in 14m2s. Using only -lmkl_em64t it EAMP> runs in 14m31s. Using serial compilations it ran in 12m20s. you should also compare against the parallel executable run with -np 1 against the serial executable. depending on your hardware (memory speed) and the fact that the 10.0 MKL has about 20% speed improvement on recent cpus, it is quite possible. since your problem is quite large, i guess that a lot of time is spent in the libraries. with a single quad-core cpu you also have the maximum amount of memory contention when running 4 individual mpi threads, whereas using multi-threading may take better advantage of data locality and reduce the load on the memory bus. cheers, axel. EAMP> EAMP> EAMP> EAMP> Thanks, EAMP> Eduardo EAMP> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From akohlmey at cmm.chem.upenn.edu Wed May 7 00:21:01 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 6 May 2008 18:21:01 -0400 (EDT) Subject: [Pw_forum] openmp vs mpich performance with MKL 10.x In-Reply-To: References: Message-ID: On Tue, 6 May 2008, Eduardo Ariel Menendez Proupin wrote: EAMP> Dear Axel, EAMP> EAMP> > you should also compare against the parallel executable EAMP> > run with -np 1 against the serial executable. EAMP> EAMP> It is a bit slower. eduardo, ok. thanks, here are some timing results on my desktop. the machine was not entirely idle and freshly booted, so take the numbers with a bit of caution. i have a one year old two-socket intel dual core 2.66GHz machine (i.e. more or less equivalent to a single socket intel quad-core, with two dual-core dies in one case). this is using the latest cvs code: with serial MKL, serial FFTW-2.1.5 and OpenMPI with 4 mpi tasks. i get a wall time of 12m12s and cpu time of 10m40s. changing MKL to threaded MKL using 4 threads and 1 mpi task i get a wall time of 18m8s and cpu time of 28m30s (which means that roughly 40% of the time the code was running multi-threaded BLAS/LAPACK). with serial FFT, threaded MKL using 2 threads and 2 mpi tasks i get a wall time of 12m45s and cpu time of 14.42s now when i swap the serial FFTW2 against the intel MKL FFTW2 wrapper i get with 2 threads and 2 MPI tasks a wall time of 15m2s and a cpu time of 24m11s. and with 4 threads and 1 MPI task i get a wall time of 0h19m and a cpu time of 1h 2m and finally when disabling threading and with 4 MPI tasks i get 12m38 wall time and 11m14s cpu time. obviously, switching to the intel fft didn't help. your system with many states and only gamma point is definitely a case that benefits the most from multi-threaded BLAS/LAPACK. i'm curious to learn how these number match up with your performance measurements. cheers, axel. EAMP> EAMP> Attached is my input. EAMP> EAMP> EAMP> EAMP> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From degironc at sissa.it Wed May 7 10:36:27 2008 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 07 May 2008 10:36:27 +0200 Subject: [Pw_forum] comparing gaussian03 with pwscf In-Reply-To: References: Message-ID: <48216A0B.9000909@sissa.it> how to carve an atom from a molecule or a solid is a long standing problem with no clear solution basically due to the fact that it is an ill defined problem as . however I think that Bader analysis, based on defining atomic volumes from topological properties of the charge density rather than just nearest-neighbhor interatomic distances, give results that are more consistent with chemical intuition. I remember for instance that in GaAs a description based on Voronoy polyhedra would assign higher charge to Ga than to As just because the As is "fatter" than Ga and a fraction of the charge that one would visually assign to it was in the Ga territory... An analysis based on Bader decomposition was instead consistent with the expectation. Unfortunately Bader analysis is not presently implemented among QE post-processing tools. Other options to try to assign charges to atoms are Lowdin population analysis (it however depends on the choice of atomic functions used) or construction of maximally localized Wannier functions that would help splitting the charge density in contributions with well identified origin... both these two schemes are available using QE and/or wannier90 code. hope this helps, stefano Eduardo Ariel Menendez Proupin wrote: > If there is doubt on the approximations for lantanides, I suggest to > make some tests with something more "classic", such as NaCl or MgO and > then compare PWSCF vs GAUSSIAN with complete basis sets. > > One question? What is the useful information provided by the knowledge > of the charge transfer? Can it be correlated to any measurable > property (reactivity, entropy, adsorcion enrgy, ....) or with any > measurable and difficult to calculate property? > > Some years ago I calculated and reported some charge transfer and said > something about the ionicity. To know better, I calculated the charge > transfer in NaCl. For this, I integrated the charge density in the > Voronoi cells of Na and Cl, using the self consisten charge density > and the superposition of atomic densities. The difference is the > charge transfer or, more precisely, the charge that crosses the > boundary of the Voronoi cells. > To my surprise, the charge transfer in NaCl is 0.1 electron, and not 1 > electron as the textbooks suggest. I also tested it with MgO (0.2 > instead of 2). So, where is hidden the truth of the ionic bond? > > > > -- > Eduardo Menendez > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From eariel99 at gmail.com Wed May 7 23:06:26 2008 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Wed, 7 May 2008 17:06:26 -0400 Subject: [Pw_forum] Fwd: openmp vs mpich performance with MKL 10.x In-Reply-To: References: Message-ID: ---------- Forwarded message ---------- From: Eduardo Ariel Menendez Proupin Date: 2008/5/7 Subject: Re: [Pw_forum] openmp vs mpich performance with MKL 10.x To: Axel Kohlmeyer Hi, with serial MKL, serial FFTW-2.1.5 and OpenMPI with 4 mpi tasks. > i get a wall time of 12m12s and cpu time of 10m40s. > I GET OMP_NUM_THREADS=1 MKL_NUM_THREADS=1 DFLAGS = -D__INTEL -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA mpiexec -n 4 /home/emenendez/ChemUtils/Espresso/espresso4.0cvs3/bin4/pw.x < cdteo0.2.md.in >> cdteo0.2.md.out PWSCF : 12m33.73s CPU time, 12m43.31s wall time > changing MKL to threaded MKL using 4 threads and 1 mpi task > i get a wall time of 18m8s and cpu time of 28m30s > (which means that roughly 40% of the time the code > was running multi-threaded BLAS/LAPACK). OMP_NUM_THREADS=4 MKL_NUM_THREADS=4 mpiexec -n 1 /home/emenendez/ChemUtils/Espresso/espresso4.0cvs3/bin4/pw.x < cdteo0.2.md.in >> cdteo0.2.md.out PWSCF : 27m40.02s CPU time, 17m 2.73s wall time > > with serial FFT, threaded MKL using 2 threads and 2 mpi tasks > i get a wall time of 12m45s and cpu time of 14.42s UNTESTED IN THIS MACHINE, BUT WORSE IN OTHERS. > > now when i swap the serial FFTW2 against the > intel MKL FFTW2 wrapper i get with 2 threads and 2 MPI tasks > a wall time of 15m2s and a cpu time of 24m11s. UNTESTED IN THIS MACHINE, BUT WORSE IN OTHERS. > and with 4 threads and 1 MPI task i get > a wall time of 0h19m and a cpu time of 1h 2m OMP_NUM_THREADS=4 MKL_NUM_THREADS=4 mpiexec -n 1 /home/emenendez/ChemUtils/Espresso/espresso4.0cvs3/bin5/pw.x < cdteo0.2.md.in >> cdteo0.2.md.out PWSCF : 58m50.42s CPU time, 17m55.90s wall time > and finally when disabling threading and with > 4 MPI tasks i get 12m38 wall time and 11m14s cpu time. OMP_NUM_THREADS=1 MKL_NUM_THREADS=1 DFLAGS = -D__INTEL -D__FFTW -D__MPI -D__PARA (using fftw2_intel) mpiexec -n 4 /home/emenendez/ChemUtils/Espresso/espresso4.0cvs3/bin5/pw.x < cdteo0.2.md.in >> cdteo0.2.md.out PWSCF : 13m 2.54s CPU time, 13m16.11s wall time IT IS WORSE THAN USING THE INTERNAL FFTW. HOWEVER, RUNNING SERIAL OMP_NUM_THREADS=4 MKL_NUM_THREADS=4 DFLAGS = -D__INTEL -D__FFTW BLAS_LIBS = -lfftw2xf_intel -lmkl_em64t /home/emenendez/ChemUtils/Espresso/espresso4.0cvs3/bin2/pw.x < cdteo0.2.md.in >> cdteo0.2.md.out PWSCF : 36m58.97s CPU time, 11m36.11s wall time OMP_NUM_THREADS=4 MKL_NUM_THREADS=4 DFLAGS = -D__INTEL -D__FFTW3 BLAS_LIBS = -lfftw3xf_intel -lmkl_em64t /home/emenendez/ChemUtils/Espresso/espresso4.0cvs3/bin3/pw.x < cdteo0.2.md.in >> cdteo0.2.md.out PWSCF : 36m44.64s CPU time, 11m29.59s wall time > > obviously, switching to the intel fft didn't help. FOR ME, IT HELPS ONLY WHEN RUNNING SERIAL. > > > your system with many states and only gamma point > is definitely a case that benefits the most from > multi-threaded BLAS/LAPACK. TYPICAL FOR BO MOLECULAR DYNAMICS. I WOULD SAY, AVOID MIXING MPI AND OPENMP. ALSO AVOID INTEL FFTW WRAPPERS WITH MPI, EVEN IF OMP_NUM_THREADS=1. USE THREADED BLAS/LAPACK/FFTW2(3) FOR SERIAL RUNS. ANYWAY, THE DIFFERENCE BETWEEN THE BEST MPI AND THE BEST OPENMP IS LESS THAN 10% (11m30s vs 12m43s) > > > i'm curious to learn how these number match up > with your performance measurements. > > cheers, > axel. > > > -- Eduardo Menendez -- Eduardo Menendez -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080507/319e20ea/attachment.htm -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: make.sys.txt Url: http://www.democritos.it/pipermail/pw_forum/attachments/20080507/319e20ea/attachment.txt From eariel99 at gmail.com Wed May 7 23:40:05 2008 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Wed, 7 May 2008 17:40:05 -0400 Subject: [Pw_forum] comparing gaussian03 with pwscf In-Reply-To: References: Message-ID: Hi, Bader anaylisis is well founded, but when I read of it I did not like two things. One is that Bader atoms have strange shapes sometimes. Well, this is subjective, and easier to understand than the collapse of the wavefunction. The second that it is still a partition of the space, and it depends more on the size of the atoms than on the charge transfer. As the valence charge density changes really little, the total charge density changes proportionally even less. I suspect that the atomic boundaries change little during the self-consistent calculations, and if one performs a Bader analysis with the self-consistent wave functions or with the charge density obtained from the superposition of the the neutral atomic charge densities, the assigned atomic charges are the almost the same. Hence an oxygen can have a charge near -2 with and without self-consistency, but this is due to the size of the atoms, and not its affinity to trap electrons or the polarization of the bonds. I have not made Bader analysis because because it is not implemented in the codes that I have worked with, and I may have missed some important article. Voronoy assigned charge depend on the atomic radius used: covalent, ionic. One can also obtain the proyected densities of states and integrate them to the Fermi level to obtain the charges. I did that once, and I chose whether to use covalent or atomic radii guided by the "principle" that oxygen must be negatively charged. I would make some effort to study this topic if I knew what is the real importance of quantifiying the charge transfer. Regards EM *Stefano de Gironcoli* *Wed May 7 10:36:27 CEST 2008* how to carve an atom from a molecule or a solid is a long standing problem with no clear solution basically due to the fact that it is an ill defined problem as .however I think that Bader analysis, based on defining atomic volumesfrom topological properties of the charge density rather than justnearest-neighbhor interatomic distances, give results that are more consistent with chemical intuition.I remember for instance that in GaAs a description based on Voronoy polyhedra would assign higher charge to Ga than to As just because the As is "fatter" than Ga and a fraction of the charge that one would visually assign to it was in the Ga territory... An analysis based on Bader decomposition was instead consistent with the expectation. Unfortunately Bader analysis is not presently implemented among QE post-processing tools. Other options to try to assign charges to atoms are Lowdin population analysis (it however depends on the choice of atomic functions used) or construction of maximally localized Wannier functions that would help splitting the charge density in contributions with well identified origin... both these two schemes are available using QE and/or wannier90 code. hope this helps, stefano 2008/5/6 Eduardo Ariel Menendez Proupin : > If there is doubt on the approximations for lantanides, I suggest to make > some tests with something more "classic", such as NaCl or MgO and then > compare PWSCF vs GAUSSIAN with complete basis sets. > > One question? What is the useful information provided by the knowledge of > the charge transfer? Can it be correlated to any measurable property > (reactivity, entropy, adsorcion enrgy, ....) or with any measurable and > difficult to calculate property? > > Some years ago I calculated and reported some charge transfer and said > something about the ionicity. To know better, I calculated the charge > transfer in NaCl. For this, I integrated the charge density in the Voronoi > cells of Na and Cl, using the self consisten charge density and the > superposition of atomic densities. The difference is the charge transfer or, > more precisely, the charge that crosses the boundary of the Voronoi cells. > To my surprise, the charge transfer in NaCl is 0.1 electron, and not 1 > electron as the textbooks suggest. I also tested it with MgO (0.2 instead of > 2). So, where is hidden the truth of the ionic bond? > > > > -- > Eduardo Menendez > -- Eduardo Menendez -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080507/d87847a5/attachment-0001.htm From akohlmey at cmm.chem.upenn.edu Wed May 7 23:47:43 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 7 May 2008 17:47:43 -0400 (EDT) Subject: [Pw_forum] openmp vs mpich performance with MKL 10.x In-Reply-To: References: Message-ID: On Wed, 7 May 2008, Eduardo Ariel Menendez Proupin wrote: EAM> Hi, EAM> Plese, find attached my best make.sys, to be run serially. Try this in your EAM> system. My timings are close to yours. Below are the details. However, it ok, i tried running on my machine with the intel wrapper i get a wall time of 13m43s and using a multi-threaded fftw3 i need a wall time of 16m13s to complete the job, but i have not yet added the additional tunings that i added to CPMD that finally made fftw3 faster. in summary it looks as if on my hardware MPI is the winner. i would be interested to see if you get different timings with OpenMPI instead of MPICH. EAM> runs faster serially than using mpiexec -n 1. [...] EAM> > EAM> > obviously, switching to the intel fft didn't help. EAM> EAM> FOR ME, IT HELPS ONLY WHEN RUNNING SERIAL. on CPMD i found that actually, using the multi-threaded fftw3 is _even_ faster. you will need to add one function call to tell the fftw3-planner that all future plans should be generated for $OMP_NUM_THREADS threads. the fact that it helps in the serial code only, is easily understandable if you look what QEs FFT modules do differently when running in serial or in parallel. if you run in serial, QE calls a 3d-FFT directly instead of a sequence of 1d/2d-FFTs. with the 3d-fft you have the chance to parallelize in the same was as with MPI by using threads. if you run in parallel, you already call many small 1d-ffts and those don't parallelize well. instead it would be required to distribute those calls across threads to have a similar gain. EAM> > your system with many states and only gamma point EAM> > is definitely a case that benefits the most from EAM> > multi-threaded BLAS/LAPACK. EAM> EAM> TYPICAL FOR BO MOLECULAR DYNAMICS. EAM> I WOULD SAY, AVOID MIXING MPI AND OPENMP. ALSO AVOID INTEL FFTW WRAPPERS EAM> WITH MPI, EVEN IF OMP_NUM_THREADS=1. EAM> USE THREADED BLAS/LAPACK/FFTW2(3) FOR SERIAL RUNS. i don't think that this can be said in general, because your system is a best case scenario. in my experience a serial executable is about 10% faster than a parallel one for one task with plane-wave pseudopotential calculations. the fact that you have a large system with only gamma point gives you the maximum benefit from parallel LAPACK/BLAS and the multi-threaded FFT. however, if you want to do BO-dynamics i suspect that you may lose the performance advantage, since the wavefunction extrapolation will cut down the number of SCF cycles needed and at the same time the force calculation is not multi-threaded at all. to get a real benefit from a multi-core machine, additional OpenMP directives need to be added to the QE code. the fact that OpenMP libraries and MPI parallelization are somewhat comparable, could indicate that there is some more room to improve the MPI parallelization. luckily for most QE-users the first, simple level of parallelization across k-points will apply and give them a lot of speedup without much and only _then_ the parallelization across the G-space, task groups and finally threads/libraries/OpenMP directives should apply. cheers, axel. EAM> EAM> ANYWAY, THE DIFFERENCE BETWEEN THE BEST MPI AND THE BEST OPENMP IS LESS THAN EAM> 10% (11m30s vs 12m43s) EAM> EAM> > EAM> > EAM> > i'm curious to learn how these number match up EAM> > with your performance measurements. EAM> > EAM> > cheers, EAM> > axel. EAM> > EAM> > EAM> > EAM> EAM> EAM> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From Mohamed.Majdoub at mail.uh.edu Thu May 8 20:51:05 2008 From: Mohamed.Majdoub at mail.uh.edu (Mohamed.Majdoub at mail.uh.edu) Date: Thu, 08 May 2008 13:51:05 -0500 Subject: [Pw_forum] Au relaxation error Message-ID: Dear users, Thanks professor I am a new pwscf user. I have been trying to do a geometry relaxation of a gold nanocluster (few wunit cells of Au). The objective is to put this metal in contact with an MgO insulator and relax the 2 structures to find out the optimal interface configuration. As a first trial, I am relaxing only the Au alone. But I keep getting error message. The Au has fcc unit cell with lattice constant 4.0783 angstrom = 7.70687 a.u. ? calculation = "relax", ? pseudo_dir? = "/pwscf/pseudo", ? outdir????? = "/pwscf/pwscftemp", / &SYSTEM ? ibrav?????? = 2, ? celldm(1)?? = 7.6533D0, ? nat???????? = 36, ? ntyp??????? = 1, ? ecutwfc???? = 30.D0, ? occupations = "smearing", ? smearing??? = "gaussian", ? degauss???? = 0.005D0, / &ELECTRONS ? conv_thr??? = 1.D-6, ? mixing_beta = 0.3D0, / &IONS ? pot_extrapolation = "second_order", ? wfc_extrapolation = "second_order", / ATOMIC_SPECIES Au? 196.96655? Au.pz-d-van.UPF ATOMIC_POSITIONS angstrom Au???????? 0.00000??????? 0.00000?????? -0.00000 Au???????? 0.00000??????? 2.03915??????? 2.03915 Au???????? 2.03915??????? 0.00000??????? 2.03915 Au???????? 2.03915??????? 2.03915??????? 0.00000 Au???????? 4.07830??????? 0.00000?????? -0.00000 Au???????? 4.07830??????? 2.03915??????? 2.03915 Au???????? 0.00000??????? 4.07830?????? -0.00000 Au???????? 2.03915??????? 4.07830??????? 2.03915 Au???????? 0.00000??????? 0.00000??????? 4.07830 Au???????? 0.00000??????? 2.03915??????? 6.11745 Au???????? 2.03915??????? 0.00000??????? 6.11745 Au???????? 2.03915??????? 2.03915??????? 4.07830 Au???????? 0.00000??????? 4.07830??????? 4.07830 Au???????? 2.03915??????? 4.07830??????? 6.11745 Au???????? 4.07830??????? 0.00000??????? 4.07830 Au???????? 4.07830??????? 2.03915??????? 6.11745 Au???????? 4.07830??????? 4.07830?????? -0.00000 Au???????? 4.07830??????? 4.07830??????? 4.07830 Au???????? 0.00000??????? 0.00000??????? 8.15660 Au???????? 0.00000??????? 2.03915?????? 10.19575 Au???????? 2.03915??????? 0.00000?????? 10.19575 Au???????? 2.03915??????? 2.03915??????? 8.15660 Au???????? 0.00000??????? 0.00000?????? 12.23490 Au???????? 0.00000??????? 2.03915?????? 14.27405 Au???????? 2.03915??????? 0.00000?????? 14.27405 Au???????? 2.03915??????? 2.03915?????? 12.23490 Au???????? 0.00000??????? 4.07830??????? 8.15660 Au???????? 2.03915??????? 4.07830?????? 10.19575 Au???????? 0.00000??????? 4.07830?????? 12.23490 Au???????? 2.03915??????? 4.07830?????? 14.27405 Au???????? 4.07830??????? 0.00000??????? 8.15660 Au???????? 4.07830??????? 2.03915?????? 10.19575 Au???????? 4.07830??????? 0.00000?????? 12.23490 Au???????? 4.07830??????? 2.03915?????? 14.27405 Au???????? 4.07830??????? 4.07830??????? 8.15660 Au???????? 4.07830??????? 4.07830?????? 12.23490 K_POINTS automatic 6 6 1 0 0 0 ---------------------------------------------------------------------------- ?? warning: symmetry operation #? 2 not allowed.?? fractional translation: ?????? 0.0139992 -0.0139992? 0.0000000? in crystal coordinates ???? warning: symmetry operation #? 7 not allowed.?? fractional translation: ?????? 0.0069996 -0.0069996 -0.0069996? in crystal coordinates ???? warning: symmetry operation #? 8 not allowed.?? fractional translation: ?????? 0.0069996 -0.0069996? 0.0069996? in crystal coordinates ???? warning: symmetry operation # 27 not allowed.?? fractional translation: ?????? 0.0069996 -0.0069996 -0.0069996? in crystal coordinates ???? warning: symmetry operation # 28 not allowed.?? fractional translation: ?????? 0.0069996 -0.0069996? 0.0069996? in crystal coordinates ???? warning: symmetry operation # 29 not allowed.?? fractional translation: ?????? 0.0139992 -0.0139992? 0.0000000? in crystal coordinates ....... ? Initial potential from superposition of free atoms ???? starting charge? 395.74037, renormalised to? 396.00000 ???? Starting wfc are atomic ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ???? from cdiaghg : error #?????? 325 ???? info =/= 0 ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ???? stopping ... ------------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080508/ad3bdf59/attachment.htm From akohlmey at cmm.chem.upenn.edu Thu May 8 21:04:43 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Thu, 8 May 2008 15:04:43 -0400 (EDT) Subject: [Pw_forum] Au relaxation error In-Reply-To: References: Message-ID: On Thu, 8 May 2008, Mohamed.Majdoub at mail.uh.edu wrote: MM> Dear users, mohamed, please _first_ study the online documentation, troubleshooting tips and the mailing list archives. this error is one of the most frequently reported ones... cheers, axel. p.s.: ...and while you are at it, please consider the policy here to state your name and affiliation. thanks. MM> MM> ---------------------------------------------------------------------------- MM> ?? warning: symmetry operation #? 2 not allowed.?? fractional translation: MM> ?????? 0.0139992 -0.0139992? 0.0000000? in crystal coordinates MM> ???? warning: symmetry operation #? 7 not allowed.?? fractional translation: MM> ?????? 0.0069996 -0.0069996 -0.0069996? in crystal coordinates MM> ???? warning: symmetry operation #? 8 not allowed.?? fractional translation: MM> ?????? 0.0069996 -0.0069996? 0.0069996? in crystal coordinates MM> ???? warning: symmetry operation # 27 not allowed.?? fractional translation: MM> ?????? 0.0069996 -0.0069996 -0.0069996? in crystal coordinates MM> ???? warning: symmetry operation # 28 not allowed.?? fractional translation: MM> ?????? 0.0069996 -0.0069996? 0.0069996? in crystal coordinates MM> ???? warning: symmetry operation # 29 not allowed.?? fractional translation: MM> ?????? 0.0139992 -0.0139992? 0.0000000? in crystal coordinates MM> ....... MM> MM> ? Initial potential from superposition of free atoms MM> MM> ???? starting charge? 395.74037, renormalised to? 396.00000 MM> ???? Starting wfc are atomic MM> MM> ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% MM> ???? from cdiaghg : error #?????? 325 MM> ???? info =/= 0 MM> ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% MM> MM> ???? stopping ... MM> ------------------------------------------------------------------------ MM> MM> MM> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From weic at Princeton.EDU Thu May 8 23:39:29 2008 From: weic at Princeton.EDU (Wei Chen (weic@Princeton.EDU)) Date: Thu, 08 May 2008 17:39:29 -0400 Subject: [Pw_forum] Definition of the projector function output in the "file_beta" file by LD1. Message-ID: Dear Paolo: I am wondering about the definition of the projector function output in the "file_beta" file produced by LD1. Is it defined as the TRUE beta function multiplied by r ? (Just like the AE and PS radial wavefunctions output in ld1.wfc and ld1ps.wfc are actually the TRUE radial wavefunctions multiplied by r. ) I guess this is the case, because the true projector function needs to satisfy < projector_i | \phi^PS_j > = \delta_ij. where \phi^PS_j is the PS partial wave. I checked with the output of "file_beta" (\beta_i ), and ld1ps.wfc (\phi^PS_j), and I found the following is true: \int (\beta_i / r ) * (\phi^PS_i / r ) * r^2 dr = 1 Am I right about the output in the "file_beta" file? Thank you very much for your kind clarification and help! Wei Chen Email: weic at princeton.edu Princeton University From j.antonio.montoya at gmail.com Fri May 9 00:11:07 2008 From: j.antonio.montoya at gmail.com (Javier Antonio Montoya) Date: Thu, 8 May 2008 18:11:07 -0400 Subject: [Pw_forum] Pseudoptential for Nd Message-ID: <993c5eba0805081511t66fe60f8g7d19eb9f1e36d60a@mail.gmail.com> Dear all, Is there anyone in the forum who can provide me with a pseudo-potential (nonlinear core-correction + ultrasoft + PBE) for any of the following elements? : Sm, Nd, Pr, Ce . We are running experiments that include those elements and I could provide feedback on how well those pseudos reproduce experimental properties, such as vibrational spectra and lattice parameters at different pressure conditions; in order to include them in the PWscf.org web page. Nd is the one that we are going to measure first, so, getting that one would be cool. Thanks, Javier -- Javier A. Montoya Geophysical Laboratory Carnegie Institution of Washington 5251 Broad Branch Rd. NW Washington, DC 20015 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080508/6b380739/attachment.htm From paulatto at sissa.it Fri May 9 09:54:36 2008 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 9 May 2008 09:54:36 +0200 (CEST) Subject: [Pw_forum] Definition of the projector function output in the "file_beta" file by LD1. In-Reply-To: References: Message-ID: <5305.147.122.5.216.1210319676.squirrel@webmail.sissa.it> On Thu, May 8, 2008 23:39, Wei Chen (weic at Princeton.EDU) wrote: > Am I right about the output in the "file_beta" file? Dear Wei Chen, you are right, the condition is: <\beta_i|\psi^PS_j> = \delta_{i,j}. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) +39 040 3787 511 http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From degironc at sissa.it Fri May 9 12:31:01 2008 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 09 May 2008 12:31:01 +0200 Subject: [Pw_forum] Au relaxation error In-Reply-To: References: Message-ID: <482427E5.2010801@sissa.it> Dear Mohamed Majdoub, have you checked your structure with some visualization tool like xcrysden or similar ? remember that celldm(1) is given in bohr radii (7.6 a.u., about 4 Angstrom) while your atomic positions, given in angstrom, extend from 0 to 14 Angstrom.. it seems to me quite unlikely that your structure is what you think it is. hope it helps, stefano de Gironcoli - SISSA and DEMOCRITOS Mohamed.Majdoub at mail.uh.edu wrote: > Dear users, > > Thanks professor > I am a new pwscf user. I have been trying to do a geometry relaxation > of a gold nanocluster (few wunit cells of Au). The objective is to put > this metal in contact with an MgO insulator and relax the 2 structures > to find out the optimal interface configuration. As a first trial, I > am relaxing only the Au alone. But I keep getting error message. The > Au has fcc unit cell with lattice constant 4.0783 angstrom = 7.70687 a.u. > > calculation = "relax", > pseudo_dir = "/pwscf/pseudo", > outdir = "/pwscf/pwscftemp", > / > &SYSTEM > ibrav = 2, > celldm(1) = 7.6533D0, > nat = 36, > ntyp = 1, > ecutwfc = 30.D0, > occupations = "smearing", > smearing = "gaussian", > degauss = 0.005D0, > / > &ELECTRONS > conv_thr = 1.D-6, > mixing_beta = 0.3D0, > / > &IONS > pot_extrapolation = "second_order", > wfc_extrapolation = "second_order", > / > ATOMIC_SPECIES > Au 196.96655 Au.pz-d-van.UPF > ATOMIC_POSITIONS angstrom > Au 0.00000 0.00000 -0.00000 > Au 0.00000 2.03915 2.03915 > Au 2.03915 0.00000 2.03915 > Au 2.03915 2.03915 0.00000 > Au 4.07830 0.00000 -0.00000 > Au 4.07830 2.03915 2.03915 > Au 0.00000 4.07830 -0.00000 > Au 2.03915 4.07830 2.03915 > Au 0.00000 0.00000 4.07830 > Au 0.00000 2.03915 6.11745 > Au 2.03915 0.00000 6.11745 > Au 2.03915 2.03915 4.07830 > Au 0.00000 4.07830 4.07830 > Au 2.03915 4.07830 6.11745 > Au 4.07830 0.00000 4.07830 > Au 4.07830 2.03915 6.11745 > Au 4.07830 4.07830 -0.00000 > Au 4.07830 4.07830 4.07830 > Au 0.00000 0.00000 8.15660 > Au 0.00000 2.03915 10.19575 > Au 2.03915 0.00000 10.19575 > Au 2.03915 2.03915 8.15660 > Au 0.00000 0.00000 12.23490 > Au 0.00000 2.03915 14.27405 > Au 2.03915 0.00000 14.27405 > Au 2.03915 2.03915 12.23490 > Au 0.00000 4.07830 8.15660 > Au 2.03915 4.07830 10.19575 > Au 0.00000 4.07830 12.23490 > Au 2.03915 4.07830 14.27405 > Au 4.07830 0.00000 8.15660 > Au 4.07830 2.03915 10.19575 > Au 4.07830 0.00000 12.23490 > Au 4.07830 2.03915 14.27405 > Au 4.07830 4.07830 8.15660 > Au 4.07830 4.07830 12.23490 > K_POINTS automatic > 6 6 1 0 0 0 > > > ---------------------------------------------------------------------------- > > warning: symmetry operation # 2 not allowed. fractional translation: > 0.0139992 -0.0139992 0.0000000 in crystal coordinates > warning: symmetry operation # 7 not allowed. fractional > translation: > 0.0069996 -0.0069996 -0.0069996 in crystal coordinates > warning: symmetry operation # 8 not allowed. fractional > translation: > 0.0069996 -0.0069996 0.0069996 in crystal coordinates > warning: symmetry operation # 27 not allowed. fractional > translation: > 0.0069996 -0.0069996 -0.0069996 in crystal coordinates > warning: symmetry operation # 28 not allowed. fractional > translation: > 0.0069996 -0.0069996 0.0069996 in crystal coordinates > warning: symmetry operation # 29 not allowed. fractional > translation: > 0.0139992 -0.0139992 0.0000000 in crystal coordinates > ....... > > Initial potential from superposition of free atoms > > starting charge 395.74037, renormalised to 396.00000 > Starting wfc are atomic > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from cdiaghg : error # 325 > info =/= 0 > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From raveiga at yahoo.com Fri May 9 15:49:10 2008 From: raveiga at yahoo.com (Roberto G. A. Veiga) Date: Fri, 9 May 2008 06:49:10 -0700 (PDT) Subject: [Pw_forum] Defining an antiferromagnetic graphene nanoribbon Message-ID: <861402.84473.qm@web33503.mail.mud.yahoo.com> Dear PW users: I want to carry out a single point calculation of an antiferromagnetic graphene nanoribbon with PWscf. Since such a system is magnetic, with a specific magnetic orientation for the edge carbons, I have to perform a spin-polarized calculation. I'd like to know if the following PW input is suitable for such a calculation. &CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , pseudo_dir = '$DIR' , / &SYSTEM ibrav = 8, A = 17.482046 , B = 20.000000 , C = 15.000000 , nat = 70 , ntyp = 4, ecutwfc = 20.00 , ecutrho = 80.00 , occupations = 'smearing' , degauss = 0.01 , smearing = 'gaussian' , nspin = 2 , starting_magnetization(1) = -1.0 , starting_magnetization(2) = 1.0 , starting_magnetization(3) = 0.0 , starting_magnetization(4) = 0.0 , / &ELECTRONS conv_thr = 1.0D-6 , startingpot = 'atomic', startingwfc = 'atomic', mixing_mode = 'plain' , mixing_beta = 0.25 , diagonalization = 'david' , / ATOMIC_SPECIES C-1 12.0107 C.pbe.UPF C+1 12.0107 C.pbe.UPF C 12.0107 C.pbe.UPF H 1.0079 H.pbe.UPF ATOMIC_POSITIONS angstrom C+1 1.249543 -0.711074 0.000000 C 0.000947 -0.016393 -0.000001 C 0.000844 1.443145 -0.000001 C 1.249381 2.159954 0.000001 C 1.249409 3.608946 0.000001 C 0.000843 4.325668 -0.000001 C 0.000939 5.785283 0.000000 C-1 1.249515 6.479991 -0.000001 H 1.249981 -1.825631 0.000000 H 1.249981 7.594413 0.000000 C+1 3.746978 -0.711074 0.000000 C 2.498382 -0.016393 -0.000001 C 2.498279 1.443145 -0.000001 C 3.746816 2.159954 0.000001 C 3.746844 3.608946 0.000001 C 2.498278 4.325668 -0.000001 C 2.498374 5.785283 0.000000 C-1 3.746950 6.479991 -0.000001 H 3.747416 -1.825631 0.000000 H 3.747416 7.594413 0.000000 C+1 6.244413 -0.711074 0.000000 C 4.995817 -0.016393 -0.000001 C 4.995714 1.443145 -0.000001 C 6.244251 2.159954 0.000001 C 6.244279 3.608946 0.000001 C 4.995713 4.325668 -0.000001 C 4.995809 5.785283 0.000000 C-1 6.244385 6.479991 -0.000001 H 6.244851 -1.825631 0.000000 H 6.244851 7.594413 0.000000 C+1 8.741849 -0.711074 0.000000 C 7.493253 -0.016393 -0.000001 C 7.493150 1.443145 -0.000001 C 8.741687 2.159954 0.000001 C 8.741715 3.608946 0.000001 C 7.493149 4.325668 -0.000001 C 7.493245 5.785283 0.000000 C-1 8.741821 6.479991 -0.000001 H 8.742287 -1.825631 0.000000 H 8.742287 7.594413 0.000000 C+1 11.239284 -0.711074 0.000000 C 9.990688 -0.016393 -0.000001 C 9.990585 1.443145 -0.000001 C 11.239122 2.159954 0.000001 C 11.239150 3.608946 0.000001 C 9.990584 4.325668 -0.000001 C 9.990680 5.785283 0.000000 C-1 11.239256 6.479991 -0.000001 H 11.239722 -1.825631 0.000000 H 11.239722 7.594413 0.000000 C+1 13.736719 -0.711074 0.000000 C 12.488123 -0.016393 -0.000001 C 12.488020 1.443145 -0.000001 C 13.736557 2.159954 0.000001 C 13.736585 3.608946 0.000001 C 12.488019 4.325668 -0.000001 C 12.488115 5.785283 0.000000 C-1 13.736691 6.479991 -0.000001 H 13.737157 -1.825631 0.000000 H 13.737157 7.594413 0.000000 C+1 16.234154 -0.711074 0.000000 C 14.985558 -0.016393 -0.000001 C 14.985455 1.443145 -0.000001 C 16.233992 2.159954 0.000001 C 16.234020 3.608946 0.000001 C 14.985454 4.325668 -0.000001 C 14.985550 5.785283 0.000000 C-1 16.234126 6.479991 -0.000001 H 16.234592 -1.825631 0.000000 H 16.234592 7.594413 0.000000 K_POINTS automatic 2 1 1 0 0 0 Regards, Roberto Veiga PhD student INSA-Lyon --------------------------------- Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080509/43ac76ce/attachment.htm From Adriano.Mosca.Conte at roma2.infn.it Fri May 9 16:45:33 2008 From: Adriano.Mosca.Conte at roma2.infn.it (Adriano.Mosca.Conte at roma2.infn.it) Date: Fri, 9 May 2008 16:45:33 +0200 (CEST) Subject: [Pw_forum] Defining an antiferromagnetic graphene nanoribbon In-Reply-To: <861402.84473.qm@web33503.mail.mud.yahoo.com> References: <861402.84473.qm@web33503.mail.mud.yahoo.com> Message-ID: <53951.141.108.248.78.1210344333.squirrel@141.108.248.78> It seems ok apart some details: 1) You have to define DIR. 2) The cell parameters with ibrav=8 have to be specified by: celldm(1)=a,celldm(2)=b/a,celldm(3)=c/a 3) I'm not sure at 100% that the symbols "-" and "+" are allowed to specify atomic names. > Dear PW users: > > I want to carry out a single point calculation of an antiferromagnetic > graphene nanoribbon with PWscf. Since such a system is magnetic, with a > specific magnetic orientation for the edge carbons, I have to perform a > spin-polarized calculation. I'd like to know if the following PW input is > suitable for such a calculation. > > &CONTROL > calculation = 'scf' , > restart_mode = 'from_scratch' , > pseudo_dir = '$DIR' , > / > &SYSTEM > ibrav = 8, > A = 17.482046 , > B = 20.000000 , > C = 15.000000 , > nat = 70 , > ntyp = 4, > ecutwfc = 20.00 , > ecutrho = 80.00 , > occupations = 'smearing' , > degauss = 0.01 , > smearing = 'gaussian' , > nspin = 2 , > starting_magnetization(1) = -1.0 , > starting_magnetization(2) = 1.0 , > starting_magnetization(3) = 0.0 , > starting_magnetization(4) = 0.0 , > / > &ELECTRONS > conv_thr = 1.0D-6 , > startingpot = 'atomic', > startingwfc = 'atomic', > mixing_mode = 'plain' , > mixing_beta = 0.25 , > diagonalization = 'david' , > / > ATOMIC_SPECIES > C-1 12.0107 C.pbe.UPF > C+1 12.0107 C.pbe.UPF > C 12.0107 C.pbe.UPF > H 1.0079 H.pbe.UPF > ATOMIC_POSITIONS angstrom > C+1 1.249543 -0.711074 0.000000 > C 0.000947 -0.016393 -0.000001 > C 0.000844 1.443145 -0.000001 > C 1.249381 2.159954 0.000001 > C 1.249409 3.608946 0.000001 > C 0.000843 4.325668 -0.000001 > C 0.000939 5.785283 0.000000 > C-1 1.249515 6.479991 -0.000001 > H 1.249981 -1.825631 0.000000 > H 1.249981 7.594413 0.000000 > C+1 3.746978 -0.711074 0.000000 > C 2.498382 -0.016393 -0.000001 > C 2.498279 1.443145 -0.000001 > C 3.746816 2.159954 0.000001 > C 3.746844 3.608946 0.000001 > C 2.498278 4.325668 -0.000001 > C 2.498374 5.785283 0.000000 > C-1 3.746950 6.479991 -0.000001 > H 3.747416 -1.825631 0.000000 > H 3.747416 7.594413 0.000000 > C+1 6.244413 -0.711074 0.000000 > C 4.995817 -0.016393 -0.000001 > C 4.995714 1.443145 -0.000001 > C 6.244251 2.159954 0.000001 > C 6.244279 3.608946 0.000001 > C 4.995713 4.325668 -0.000001 > C 4.995809 5.785283 0.000000 > C-1 6.244385 6.479991 -0.000001 > H 6.244851 -1.825631 0.000000 > H 6.244851 7.594413 0.000000 > C+1 8.741849 -0.711074 0.000000 > C 7.493253 -0.016393 -0.000001 > C 7.493150 1.443145 -0.000001 > C 8.741687 2.159954 0.000001 > C 8.741715 3.608946 0.000001 > C 7.493149 4.325668 -0.000001 > C 7.493245 5.785283 0.000000 > C-1 8.741821 6.479991 -0.000001 > H 8.742287 -1.825631 0.000000 > H 8.742287 7.594413 0.000000 > C+1 11.239284 -0.711074 0.000000 > C 9.990688 -0.016393 -0.000001 > C 9.990585 1.443145 -0.000001 > C 11.239122 2.159954 0.000001 > C 11.239150 3.608946 0.000001 > C 9.990584 4.325668 -0.000001 > C 9.990680 5.785283 0.000000 > C-1 11.239256 6.479991 -0.000001 > H 11.239722 -1.825631 0.000000 > H 11.239722 7.594413 0.000000 > C+1 13.736719 -0.711074 0.000000 > C 12.488123 -0.016393 -0.000001 > C 12.488020 1.443145 -0.000001 > C 13.736557 2.159954 0.000001 > C 13.736585 3.608946 0.000001 > C 12.488019 4.325668 -0.000001 > C 12.488115 5.785283 0.000000 > C-1 13.736691 6.479991 -0.000001 > H 13.737157 -1.825631 0.000000 > H 13.737157 7.594413 0.000000 > C+1 16.234154 -0.711074 0.000000 > C 14.985558 -0.016393 -0.000001 > C 14.985455 1.443145 -0.000001 > C 16.233992 2.159954 0.000001 > C 16.234020 3.608946 0.000001 > C 14.985454 4.325668 -0.000001 > C 14.985550 5.785283 0.000000 > C-1 16.234126 6.479991 -0.000001 > H 16.234592 -1.825631 0.000000 > H 16.234592 7.594413 0.000000 > K_POINTS automatic > 2 1 1 0 0 0 > > Regards, > > Roberto Veiga > PhD student > INSA-Lyon > > > --------------------------------- > Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it > now._______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From giannozz at nest.sns.it Fri May 9 16:55:21 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 09 May 2008 16:55:21 +0200 Subject: [Pw_forum] Defining an antiferromagnetic graphene nanoribbon In-Reply-To: <53951.141.108.248.78.1210344333.squirrel@141.108.248.78> References: <861402.84473.qm@web33503.mail.mud.yahoo.com> <53951.141.108.248.78.1210344333.squirrel@141.108.248.78> Message-ID: <482465D9.6070105@nest.sns.it> Adriano.Mosca.Conte at roma2.infn.it wrote: > 3) I'm not sure at 100% that the symbols "-" and "+" are allowed to > specify atomic names. I think they are. They are read and treated as fortran character variables. Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at nest.sns.it Fri May 9 17:05:19 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 09 May 2008 17:05:19 +0200 Subject: [Pw_forum] Pseudoptential for Nd In-Reply-To: <993c5eba0805081511t66fe60f8g7d19eb9f1e36d60a@mail.gmail.com> References: <993c5eba0805081511t66fe60f8g7d19eb9f1e36d60a@mail.gmail.com> Message-ID: <4824682F.1070702@nest.sns.it> Javier Antonio Montoya wrote: > Is there anyone in the forum who can provide me with a pseudo-potential > (nonlinear core-correction + ultrasoft + PBE) for any of the following > elements? : Sm, Nd, Pr, Ce . We are running experiments that include > those elements and I could provide feedback on how well those pseudos > reproduce experimental properties, such as vibrational spectra and > lattice parameters at different pressure conditions; in order to include > them in the PWscf.org web page. Nd is the one that we are going to > measure first, so, getting that one would be cool. as I already mentioned several times in this forum: the problem with such elements is not much the pseudopotential (which IS anyway a problem: generating ultrasoft PP's for those elements is a full-time job) but the reliability of the current DFT. Years ago I tried something with Pr, with less than moderate success. I'll try to locate those files if they still exists. Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From raveiga at yahoo.com Fri May 9 17:07:23 2008 From: raveiga at yahoo.com (Roberto G. A. Veiga) Date: Fri, 9 May 2008 08:07:23 -0700 (PDT) Subject: [Pw_forum] Defining an antiferromagnetic graphene nanoribbon In-Reply-To: <53951.141.108.248.78.1210344333.squirrel@141.108.248.78> Message-ID: <375118.8711.qm@web33507.mail.mud.yahoo.com> Hi, Adriano: 1) It is defined. This input was extracted from a shell script I use to run PW. 2) Is it mandatory? PW ran without any warning, though. What I wanted is to define a chain, that is, it is periodic only along x direction. y and z are just large enough to prevent spurious interactions with the ribbon images. Is there another (better) way to specify the cell parameters for such a system? 3) It works. I already ran this input, but I was not sure if the system (a narrow graphene ribbon -- a chain -- with magnetic edges) had been defined correctly. Regards, Roberto Adriano.Mosca.Conte at roma2.infn.it wrote: It seems ok apart some details: 1) You have to define DIR. 2) The cell parameters with ibrav=8 have to be specified by: celldm(1)=a,celldm(2)=b/a,celldm(3)=c/a 3) I'm not sure at 100% that the symbols "-" and "+" are allowed to specify atomic names. > Dear PW users: > > I want to carry out a single point calculation of an antiferromagnetic > graphene nanoribbon with PWscf. Since such a system is magnetic, with a > specific magnetic orientation for the edge carbons, I have to perform a > spin-polarized calculation. I'd like to know if the following PW input is > suitable for such a calculation. > > &CONTROL > calculation = 'scf' , > restart_mode = 'from_scratch' , > pseudo_dir = '$DIR' , > / > &SYSTEM > ibrav = 8, > A = 17.482046 , > B = 20.000000 , > C = 15.000000 , > nat = 70 , > ntyp = 4, > ecutwfc = 20.00 , > ecutrho = 80.00 , > occupations = 'smearing' , > degauss = 0.01 , > smearing = 'gaussian' , > nspin = 2 , > starting_magnetization(1) = -1.0 , > starting_magnetization(2) = 1.0 , > starting_magnetization(3) = 0.0 , > starting_magnetization(4) = 0.0 , > / > &ELECTRONS > conv_thr = 1.0D-6 , > startingpot = 'atomic', > startingwfc = 'atomic', > mixing_mode = 'plain' , > mixing_beta = 0.25 , > diagonalization = 'david' , > / > ATOMIC_SPECIES > C-1 12.0107 C.pbe.UPF > C+1 12.0107 C.pbe.UPF > C 12.0107 C.pbe.UPF > H 1.0079 H.pbe.UPF > ATOMIC_POSITIONS angstrom > C+1 1.249543 -0.711074 0.000000 > C 0.000947 -0.016393 -0.000001 > C 0.000844 1.443145 -0.000001 > C 1.249381 2.159954 0.000001 > C 1.249409 3.608946 0.000001 > C 0.000843 4.325668 -0.000001 > C 0.000939 5.785283 0.000000 > C-1 1.249515 6.479991 -0.000001 > H 1.249981 -1.825631 0.000000 > H 1.249981 7.594413 0.000000 > C+1 3.746978 -0.711074 0.000000 > C 2.498382 -0.016393 -0.000001 > C 2.498279 1.443145 -0.000001 > C 3.746816 2.159954 0.000001 > C 3.746844 3.608946 0.000001 > C 2.498278 4.325668 -0.000001 > C 2.498374 5.785283 0.000000 > C-1 3.746950 6.479991 -0.000001 > H 3.747416 -1.825631 0.000000 > H 3.747416 7.594413 0.000000 > C+1 6.244413 -0.711074 0.000000 > C 4.995817 -0.016393 -0.000001 > C 4.995714 1.443145 -0.000001 > C 6.244251 2.159954 0.000001 > C 6.244279 3.608946 0.000001 > C 4.995713 4.325668 -0.000001 > C 4.995809 5.785283 0.000000 > C-1 6.244385 6.479991 -0.000001 > H 6.244851 -1.825631 0.000000 > H 6.244851 7.594413 0.000000 > C+1 8.741849 -0.711074 0.000000 > C 7.493253 -0.016393 -0.000001 > C 7.493150 1.443145 -0.000001 > C 8.741687 2.159954 0.000001 > C 8.741715 3.608946 0.000001 > C 7.493149 4.325668 -0.000001 > C 7.493245 5.785283 0.000000 > C-1 8.741821 6.479991 -0.000001 > H 8.742287 -1.825631 0.000000 > H 8.742287 7.594413 0.000000 > C+1 11.239284 -0.711074 0.000000 > C 9.990688 -0.016393 -0.000001 > C 9.990585 1.443145 -0.000001 > C 11.239122 2.159954 0.000001 > C 11.239150 3.608946 0.000001 > C 9.990584 4.325668 -0.000001 > C 9.990680 5.785283 0.000000 > C-1 11.239256 6.479991 -0.000001 > H 11.239722 -1.825631 0.000000 > H 11.239722 7.594413 0.000000 > C+1 13.736719 -0.711074 0.000000 > C 12.488123 -0.016393 -0.000001 > C 12.488020 1.443145 -0.000001 > C 13.736557 2.159954 0.000001 > C 13.736585 3.608946 0.000001 > C 12.488019 4.325668 -0.000001 > C 12.488115 5.785283 0.000000 > C-1 13.736691 6.479991 -0.000001 > H 13.737157 -1.825631 0.000000 > H 13.737157 7.594413 0.000000 > C+1 16.234154 -0.711074 0.000000 > C 14.985558 -0.016393 -0.000001 > C 14.985455 1.443145 -0.000001 > C 16.233992 2.159954 0.000001 > C 16.234020 3.608946 0.000001 > C 14.985454 4.325668 -0.000001 > C 14.985550 5.785283 0.000000 > C-1 16.234126 6.479991 -0.000001 > H 16.234592 -1.825631 0.000000 > H 16.234592 7.594413 0.000000 > K_POINTS automatic > 2 1 1 0 0 0 > > Regards, > > Roberto Veiga > PhD student > INSA-Lyon > > > --------------------------------- > Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it > now._______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum --------------------------------- Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080509/71deaa06/attachment.htm From akohlmey at cmm.chem.upenn.edu Fri May 9 16:46:07 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Fri, 9 May 2008 10:46:07 -0400 (EDT) Subject: [Pw_forum] Defining an antiferromagnetic graphene nanoribbon In-Reply-To: <375118.8711.qm@web33507.mail.mud.yahoo.com> References: <375118.8711.qm@web33507.mail.mud.yahoo.com> Message-ID: On Fri, 9 May 2008, Roberto G. A. Veiga wrote: RV> Hi, Adriano: roberto, RV> 3) It works. RV> RV> I already ran this input, but I was not sure if the system (a narrow RV> graphene ribbon -- a chain -- with magnetic edges) had been defined RV> correctly. well, to see if the system that you calculated is actually what you thought it is, you could use the QE postprocessing tools and dump the charge density and spin density and visualize it. if they are where they should be and the location of the atoms match what you expect, then you have a good chance that you made no serious error in the input... cheers, axel. RV> RV> Regards, RV> RV> Roberto RV> RV> Adriano.Mosca.Conte at roma2.infn.it wrote: It seems ok apart some details: RV> 1) You have to define DIR. RV> 2) The cell parameters with ibrav=8 have to be specified by: RV> celldm(1)=a,celldm(2)=b/a,celldm(3)=c/a RV> 3) I'm not sure at 100% that the symbols "-" and "+" are allowed to RV> specify atomic names. RV> RV> > Dear PW users: RV> > RV> > I want to carry out a single point calculation of an antiferromagnetic RV> > graphene nanoribbon with PWscf. Since such a system is magnetic, with a RV> > specific magnetic orientation for the edge carbons, I have to perform a RV> > spin-polarized calculation. I'd like to know if the following PW input is RV> > suitable for such a calculation. RV> > RV> > &CONTROL RV> > calculation = 'scf' , RV> > restart_mode = 'from_scratch' , RV> > pseudo_dir = '$DIR' , RV> > / RV> > &SYSTEM RV> > ibrav = 8, RV> > A = 17.482046 , RV> > B = 20.000000 , RV> > C = 15.000000 , RV> > nat = 70 , RV> > ntyp = 4, RV> > ecutwfc = 20.00 , RV> > ecutrho = 80.00 , RV> > occupations = 'smearing' , RV> > degauss = 0.01 , RV> > smearing = 'gaussian' , RV> > nspin = 2 , RV> > starting_magnetization(1) = -1.0 , RV> > starting_magnetization(2) = 1.0 , RV> > starting_magnetization(3) = 0.0 , RV> > starting_magnetization(4) = 0.0 , RV> > / RV> > &ELECTRONS RV> > conv_thr = 1.0D-6 , RV> > startingpot = 'atomic', RV> > startingwfc = 'atomic', RV> > mixing_mode = 'plain' , RV> > mixing_beta = 0.25 , RV> > diagonalization = 'david' , RV> > / RV> > ATOMIC_SPECIES RV> > C-1 12.0107 C.pbe.UPF RV> > C+1 12.0107 C.pbe.UPF RV> > C 12.0107 C.pbe.UPF RV> > H 1.0079 H.pbe.UPF RV> > ATOMIC_POSITIONS angstrom RV> > C+1 1.249543 -0.711074 0.000000 RV> > C 0.000947 -0.016393 -0.000001 RV> > C 0.000844 1.443145 -0.000001 RV> > C 1.249381 2.159954 0.000001 RV> > C 1.249409 3.608946 0.000001 RV> > C 0.000843 4.325668 -0.000001 RV> > C 0.000939 5.785283 0.000000 RV> > C-1 1.249515 6.479991 -0.000001 RV> > H 1.249981 -1.825631 0.000000 RV> > H 1.249981 7.594413 0.000000 RV> > C+1 3.746978 -0.711074 0.000000 RV> > C 2.498382 -0.016393 -0.000001 RV> > C 2.498279 1.443145 -0.000001 RV> > C 3.746816 2.159954 0.000001 RV> > C 3.746844 3.608946 0.000001 RV> > C 2.498278 4.325668 -0.000001 RV> > C 2.498374 5.785283 0.000000 RV> > C-1 3.746950 6.479991 -0.000001 RV> > H 3.747416 -1.825631 0.000000 RV> > H 3.747416 7.594413 0.000000 RV> > C+1 6.244413 -0.711074 0.000000 RV> > C 4.995817 -0.016393 -0.000001 RV> > C 4.995714 1.443145 -0.000001 RV> > C 6.244251 2.159954 0.000001 RV> > C 6.244279 3.608946 0.000001 RV> > C 4.995713 4.325668 -0.000001 RV> > C 4.995809 5.785283 0.000000 RV> > C-1 6.244385 6.479991 -0.000001 RV> > H 6.244851 -1.825631 0.000000 RV> > H 6.244851 7.594413 0.000000 RV> > C+1 8.741849 -0.711074 0.000000 RV> > C 7.493253 -0.016393 -0.000001 RV> > C 7.493150 1.443145 -0.000001 RV> > C 8.741687 2.159954 0.000001 RV> > C 8.741715 3.608946 0.000001 RV> > C 7.493149 4.325668 -0.000001 RV> > C 7.493245 5.785283 0.000000 RV> > C-1 8.741821 6.479991 -0.000001 RV> > H 8.742287 -1.825631 0.000000 RV> > H 8.742287 7.594413 0.000000 RV> > C+1 11.239284 -0.711074 0.000000 RV> > C 9.990688 -0.016393 -0.000001 RV> > C 9.990585 1.443145 -0.000001 RV> > C 11.239122 2.159954 0.000001 RV> > C 11.239150 3.608946 0.000001 RV> > C 9.990584 4.325668 -0.000001 RV> > C 9.990680 5.785283 0.000000 RV> > C-1 11.239256 6.479991 -0.000001 RV> > H 11.239722 -1.825631 0.000000 RV> > H 11.239722 7.594413 0.000000 RV> > C+1 13.736719 -0.711074 0.000000 RV> > C 12.488123 -0.016393 -0.000001 RV> > C 12.488020 1.443145 -0.000001 RV> > C 13.736557 2.159954 0.000001 RV> > C 13.736585 3.608946 0.000001 RV> > C 12.488019 4.325668 -0.000001 RV> > C 12.488115 5.785283 0.000000 RV> > C-1 13.736691 6.479991 -0.000001 RV> > H 13.737157 -1.825631 0.000000 RV> > H 13.737157 7.594413 0.000000 RV> > C+1 16.234154 -0.711074 0.000000 RV> > C 14.985558 -0.016393 -0.000001 RV> > C 14.985455 1.443145 -0.000001 RV> > C 16.233992 2.159954 0.000001 RV> > C 16.234020 3.608946 0.000001 RV> > C 14.985454 4.325668 -0.000001 RV> > C 14.985550 5.785283 0.000000 RV> > C-1 16.234126 6.479991 -0.000001 RV> > H 16.234592 -1.825631 0.000000 RV> > H 16.234592 7.594413 0.000000 RV> > K_POINTS automatic RV> > 2 1 1 0 0 0 RV> > RV> > Regards, RV> > RV> > Roberto Veiga RV> > PhD student RV> > INSA-Lyon RV> > RV> > RV> > --------------------------------- RV> > Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it RV> > now._______________________________________________ RV> > Pw_forum mailing list RV> > Pw_forum at pwscf.org RV> > http://www.democritos.it/mailman/listinfo/pw_forum RV> > RV> RV> _______________________________________________ RV> Pw_forum mailing list RV> Pw_forum at pwscf.org RV> http://www.democritos.it/mailman/listinfo/pw_forum RV> RV> RV> RV> --------------------------------- RV> Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From eariel99 at gmail.com Fri May 9 19:09:58 2008 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Fri, 9 May 2008 13:09:58 -0400 Subject: [Pw_forum] openmp vs mpich performance with MKL 10.x Message-ID: Thank you Axel, for all the time and the explanations of the deep numerical details. I will give up at his point. I am satisfied to know that I am not wasting CPU resources due to bad configuration, and I will keep both MPI and OpenMP compilations.. I will try to add to the benchmark of Nicola with CP. Best regards -- Eduardo Menendez -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080509/e749495a/attachment-0001.htm From Mohamed.Majdoub at mail.uh.edu Fri May 9 20:09:13 2008 From: Mohamed.Majdoub at mail.uh.edu (Mohamed.Majdoub at mail.uh.edu) Date: Fri, 09 May 2008 13:09:13 -0500 Subject: [Pw_forum] Au relaxation error In-Reply-To: References: Message-ID: Dear Axel, Thanks for pointing this out! I am already aware of it. I thought that we only need to specify the single unit cell parameter. For my case, I have like 6 unit cell aligned in one direction. How can I find out the new lattice parameter and symmetry of the nanostructure (6 unit cell)? Your suggestions are welcomed! Thanks in advance for your help! Mohamed Sabri Majdoub PhD candidate Mechanical Engineering University of Houston, TX,USA ----- Original Message ----- From: Axel Kohlmeyer Date: Thursday, May 8, 2008 2:34 pm Subject: Re: [Pw_forum] Au relaxation error To: Mohamed.Majdoub at mail.uh.edu Cc: pw_forum at pwscf.org > On Thu, 8 May 2008, Mohamed.Majdoub at mail.uh.edu wrote: > > MM> Dear users, > > mohamed, > > please _first_ study the online documentation, troubleshooting > tips and the mailing list archives. this error is one of the > most frequently reported ones... > > cheers, > ?? axel. > > > p.s.: ...and while you are at it, please consider the policy here > to state your name and affiliation. thanks. > > MM> > MM> ------------------------------------------------------------- > ---------------? > MM> ?? warning: symmetry operation #? 2 not allowed.?? > fractional translation: > MM> ?????? 0.0139992 -0.0139992? 0.0000000? in crystal coordinates > MM> ???? warning: symmetry operation #? 7 not allowed.?? > fractional translation: > MM> ?????? 0.0069996 -0.0069996 -0.0069996? in crystal coordinates > MM> ???? warning: symmetry operation #? 8 not allowed.?? > fractional translation: > MM> ?????? 0.0069996 -0.0069996? 0.0069996? in crystal coordinates > MM> ???? warning: symmetry operation # 27 not allowed.?? > fractional translation: > MM> ?????? 0.0069996 -0.0069996 -0.0069996? in crystal coordinates > MM> ???? warning: symmetry operation # 28 not allowed.?? > fractional translation: > MM> ?????? 0.0069996 -0.0069996? 0.0069996? in crystal coordinates > MM> ???? warning: symmetry operation # 29 not allowed.?? > fractional translation: > MM> ?????? 0.0139992 -0.0139992? 0.0000000? in crystal coordinates > MM> ....... > MM> > MM> ? Initial potential from superposition of free atoms > MM> > MM> ???? starting charge? 395.74037, renormalised to? 396.00000 > MM> ???? Starting wfc are atomic > MM> > MM> > ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%MM> ???? from cdiaghg : error #?????? 325 > MM> ???? info =/= 0 > MM> > ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%MM> > MM> ???? stopping ... > MM> ------------------------------------------------------------- > ----------- > MM> > MM> > MM> > > -- > ======================================================================= > Axel Kohlmeyer?? > akohlmey at cmm.chem.upenn.edu?? http://www.cmm.upenn.edu > ?? Center for Molecular Modeling?? -- > ?? University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA > 19104-6323 > tel: 1-215-898-1582,? fax: 1-215-573-6233,? office- > tel: 1-215-898-5425 > ======================================================================= > If you make something idiot-proof, the universe creates a better > idiot. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080509/38adc6ab/attachment.htm From konstantin_kudin at yahoo.com Fri May 9 21:10:49 2008 From: konstantin_kudin at yahoo.com (Konstantin Kudin) Date: Fri, 9 May 2008 12:10:49 -0700 (PDT) Subject: [Pw_forum] Defining an antiferromagnetic graphene nanoribbon In-Reply-To: <861402.84473.qm@web33503.mail.mud.yahoo.com> Message-ID: <242021.84114.qm@web57703.mail.re3.yahoo.com> Hi Roberto, Here is a ribbon input that works for sure: https://kiev.princeton.edu/misc/rg_07.scf.in (get PPs from the PWSCF website) Good luck! Kostya ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ From j.antonio.montoya at gmail.com Fri May 9 21:53:50 2008 From: j.antonio.montoya at gmail.com (Javier Antonio Montoya) Date: Fri, 9 May 2008 15:53:50 -0400 Subject: [Pw_forum] Pseudoptential for Nd In-Reply-To: <4824682F.1070702@nest.sns.it> References: <993c5eba0805081511t66fe60f8g7d19eb9f1e36d60a@mail.gmail.com> <4824682F.1070702@nest.sns.it> Message-ID: <993c5eba0805091253m50ba4816o308401a52d305cb3@mail.gmail.com> Hi Paolo On Fri, May 9, 2008 at 11:05 AM, Paolo Giannozzi wrote: > Javier Antonio Montoya wrote: > as I already mentioned several times in this forum: the problem with > such elements is not much the pseudopotential (which IS anyway a > problem: generating ultrasoft PP's for those elements is a full-time > job) but the reliability of the current DFT. Years ago I tried something > with Pr, with less than moderate success. I'll try to locate those > files if they still exists. > > Paolo > -- Thanks a lot, I would really appreciate if you can find your Pr pseudo, I am willing to take that risk. Same regarding the other ones, in case somebody already have them. The matter is that experimentally we already have the Raman and Infrared peak positions, plus the lattice constants, therefore, it will be pretty easy to decide whether or not the results make some sense and then, to use them to support some microscopic analysis of the physics that is going on in our samples. Each material contains a single rare-earth element but it also contains oxygen and iron, I think there isn't a big risk on using the ones available from the repository in PWscf.org for those other two, therefore I just need to satisfy the NLCC, Van-US, PBE requirement also for the rare-earths in order to make them match. Cheers, Javier. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080509/f74a2e9f/attachment.htm From akohlmey at cmm.chem.upenn.edu Fri May 9 21:39:52 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Fri, 9 May 2008 15:39:52 -0400 (EDT) Subject: [Pw_forum] Pseudoptential for Nd In-Reply-To: <993c5eba0805091253m50ba4816o308401a52d305cb3@mail.gmail.com> References: <993c5eba0805081511t66fe60f8g7d19eb9f1e36d60a@mail.gmail.com> <4824682F.1070702@nest.sns.it> <993c5eba0805091253m50ba4816o308401a52d305cb3@mail.gmail.com> Message-ID: On Fri, 9 May 2008, Javier Antonio Montoya wrote: javier, JAM> Thanks a lot, I would really appreciate if you can find your Pr pseudo, I am JAM> willing to take that risk. Same regarding the other ones, in case somebody JAM> already have them. The matter is that experimentally we already have the JAM> Raman and Infrared peak positions, plus the lattice constants, therefore, it JAM> will be pretty easy to decide whether or not the results make some sense and what paolo was pointing out is that you have a _fundamental_ problem. so even if you get a match, it will be by accident and not by design. what would that prove? only that you got lucky! yes, you want to match the experiment, but you want to match it for right reasons. i've seen this with uranium for example. it was giving reasonable results for some uranium oxide compounds at some lattice constant values but then it would just give complete crap at some others. JAM> then, to use them to support some microscopic analysis of the physics that JAM> is going on in our samples. Each material contains a single rare-earth JAM> element but it also contains oxygen and iron, I think there isn't a big risk so if you get crap for one element out of many (and i would not be so certain about iron either, that can be pretty nasty, too), how does that make your results better than if all elements would be doubtful. the only difference is that the error will be less obvious. JAM> on using the ones available from the repository in PWscf.org for those other JAM> two, therefore I just need to satisfy the NLCC, Van-US, PBE requirement also JAM> for the rare-earths in order to make them match. why? all you have to match is the functional! ...and as paolo had pointed out in some other mail, it looks like the vanderbilt type ultrasofts don't perform so well for "tricky" elements. it is definitely tricky to even get those potentials created with the vanderbilt code in a way they look reasonable to begin with. cheers, axel. JAM> JAM> Cheers, JAM> JAM> Javier. JAM> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From raveiga at yahoo.com Fri May 9 22:42:42 2008 From: raveiga at yahoo.com (Roberto G. A. Veiga) Date: Fri, 9 May 2008 13:42:42 -0700 (PDT) Subject: [Pw_forum] Defining an antiferromagnetic graphene nanoribbon In-Reply-To: <242021.84114.qm@web57703.mail.re3.yahoo.com> Message-ID: <318470.56336.qm@web33501.mail.mud.yahoo.com> Hi, Konstantin: thank you very much. Such a large cutoff (80 Ry) is necessary for convergence? Or maybe I'm using one quite small (20 Ry)... []s, Roberto Konstantin Kudin wrote: Hi Roberto, Here is a ribbon input that works for sure: https://kiev.princeton.edu/misc/rg_07.scf.in (get PPs from the PWSCF website) Good luck! Kostya ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum --------------------------------- Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080509/7fb147dd/attachment.htm From baroni at sissa.it Sat May 10 09:19:29 2008 From: baroni at sissa.it (Stefano Baroni) Date: Sat, 10 May 2008 09:19:29 +0200 Subject: [Pw_forum] Defining an antiferromagnetic graphene nanoribbon In-Reply-To: <318470.56336.qm@web33501.mail.mud.yahoo.com> References: <318470.56336.qm@web33501.mail.mud.yahoo.com> Message-ID: On May 9, 2008, at 10:42 PM, Roberto G. A. Veiga wrote: > Hi, Konstantin: > > thank you very much. Such a large cutoff (80 Ry) is necessary for > convergence? Or maybe I'm using one quite small (20 Ry)... it depends on the PP you are using, I guess, and certainly NOT on the actual structure you are studying. 80 Ry seems like an appropriate cutoff for moderately hard norm-conserving PP's, whereas 20 Ry sounds like appriate for many US PP's. In either case, you better check the aprporiateness by yourself, through thorough convergence tests. Stefano > > > []s, > > Roberto > > Konstantin Kudin wrote: > Hi Roberto, > > Here is a ribbon input that works for sure: > https://kiev.princeton.edu/misc/rg_07.scf.in > (get PPs from the PWSCF website) > > Good luck! > Kostya --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080510/ef313b14/attachment.htm From baroni at sissa.it Sat May 10 09:39:08 2008 From: baroni at sissa.it (Stefano Baroni) Date: Sat, 10 May 2008 09:39:08 +0200 Subject: [Pw_forum] Dear Professor In-Reply-To: <298208.535931210336141555.JavaMail.coremail@bj163app136.163.com> References: <13428159.528771209474323018.JavaMail.coremail@bj163app112.163.com> <298208.535931210336141555.JavaMail.coremail@bj163app136.163.com> Message-ID: <81637E55-D3B7-4551-B818-A29C4E60B588@sissa.it> On May 9, 2008, at 2:29 PM, penghua wrote: > > Dear Professor Baroni, Peng Hua: > I wrote a letter to you last week and received your letter which > gave me a lot of help about third derivative of energy related to > the phonon life calculation. Thank you very much! > Since I am a mew one in this domain ,I do not understand something > in (A. Debernardi, S. Baroni, and E. Molinari, Phys. Rev. Lett. 75, > 1819 - 1822 1995).In the formula(1)of the article ,the N is the > number of unit cells in crystal. But I think N is infinite in > crystal, thus the inverse lifetime becomes 0. Is what I thought is > wrong? this is like saying that the density (=N/V) of any material is zero, because the volume is infinite - do you see the point? The equation you are referring to gives the lifetime as the ratio between two quantities that diverge in the thermodynamic (N->infinity) limit, while the ratio tends to a well defined limit (not an unusual situation indeed). In your particular case, the denominator contains a N^3 tem. N^2 compensates the square of the third-order derivative of the energy [which, being an extensive quantity, is linear in the system size, i.e. N (E=N times energy per cell)]. The other factor N is the standard normalization factor for the number of k-points in the BZ. > How can i get N? Could you give me some explanation? In other terms, if you substitute the energy per cell for E in Eq. (1), you have just to divide by the number of special k-points you use to evaluate the sum (N^3 -> N_kpoints). > Beside if I want to calculate the inverse lifetime using the output > of d3.x, should I programmer according to the formula (1)? I really > appreciate your help. this is what we did befoe d3.x was available. no idea whatsoever about what d3.x actually calculates (the third derivatives appearing in Eq. 1, I guess, but I do not know any details of the input, etc.) > Thanks again for reading this mail. Hope this helps Stefano --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080510/a40fc97b/attachment.htm From raveiga at yahoo.com Sat May 10 18:11:41 2008 From: raveiga at yahoo.com (Roberto G. A. Veiga) Date: Sat, 10 May 2008 09:11:41 -0700 (PDT) Subject: [Pw_forum] Defining an antiferromagnetic graphene nanoribbon In-Reply-To: Message-ID: <765273.92348.qm@web33508.mail.mud.yahoo.com> Dear Stefano: I'm using Ultrasoft PPs. My question was because this cutoff (20 Ry) seemed to be appropriate for other carbonic systems. []s, Roberto Stefano Baroni wrote: On May 9, 2008, at 10:42 PM, Roberto G. A. Veiga wrote: Hi, Konstantin: thank you very much. Such a large cutoff (80 Ry) is necessary for convergence? Or maybe I'm using one quite small (20 Ry)... it depends on the PP you are using, I guess, and certainly NOT on the actual structure you are studying. 80 Ry seems like an appropriate cutoff for moderately hard norm-conserving PP's, whereas 20 Ry sounds like appriate for many US PP's. In either case, you better check the aprporiateness by yourself, through thorough convergence tests. Stefano []s, Roberto Konstantin Kudin wrote: Hi Roberto, Here is a ribbon input that works for sure: https://kiev.princeton.edu/misc/rg_07.scf.in (get PPs from the PWSCF website) Good luck! Kostya --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum --------------------------------- Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080510/1991e752/attachment-0001.htm From akohlmey at cmm.chem.upenn.edu Sat May 10 17:54:06 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sat, 10 May 2008 11:54:06 -0400 (EDT) Subject: [Pw_forum] Defining an antiferromagnetic graphene nanoribbon In-Reply-To: <765273.92348.qm@web33508.mail.mud.yahoo.com> References: <765273.92348.qm@web33508.mail.mud.yahoo.com> Message-ID: On Sat, 10 May 2008, Roberto G. A. Veiga wrote: RV> Dear Stefano: RV> RV> I'm using Ultrasoft PPs. My question was because this cutoff (20 Ry) RV> seemed to be appropriate for other carbonic systems. dear roberto, as stefano mentioned, what is appropriate depends on the individual potential(s) and the properties that you are iterested in. while 20-30ry is the usual wfc range for uspps, they also tend to require a higher density cutoff than the default 1:4 ratio that is adequate for norm-conserving pseudopotentials. there is no "automatically good" values and a "good beyond any doubt" setting is usually a huge waste of cpu time. there have been attempts to encode cutoff requirements into pseudopotential files to make this whole process a little bit less of a guesswork for unexperienced users, but for the reasons outlined above, it is very difficult to make a choice. it is one of the items, where you just have to know what you are doing and run the required tests by yourself... :-( cheers, axel. RV> RV> []s, RV> RV> Roberto RV> RV> Stefano Baroni wrote: RV> On May 9, 2008, at 10:42 PM, Roberto G. A. Veiga wrote: RV> RV> Hi, Konstantin: RV> RV> thank you very much. Such a large cutoff (80 Ry) is necessary for convergence? Or maybe I'm using one quite small (20 Ry)... RV> RV> it depends on the PP you are using, I guess, and certainly NOT on the actual structure you are studying. 80 Ry seems like an appropriate cutoff for moderately hard norm-conserving PP's, whereas 20 Ry sounds like appriate for many US PP's. In either case, you better check the aprporiateness by yourself, through thorough convergence tests. RV> RV> RV> Stefano RV> RV> RV> RV> RV> RV> []s, RV> RV> Roberto RV> RV> Konstantin Kudin wrote: Hi Roberto, RV> RV> Here is a ribbon input that works for sure: RV> https://kiev.princeton.edu/misc/rg_07.scf.in RV> (get PPs from the PWSCF website) RV> RV> Good luck! RV> Kostya RV> --- RV> Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste RV> [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) RV> RV> RV> La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget RV> RV> RV> RV> Please, if possible, don't send me MS Word or PowerPoint attachments RV> Why? See: http://www.gnu.org/philosophy/no-word-attachments.html RV> RV> RV> RV> RV> RV> RV> RV> RV> RV> RV> RV> _______________________________________________ RV> Pw_forum mailing list RV> Pw_forum at pwscf.org RV> http://www.democritos.it/mailman/listinfo/pw_forum RV> RV> RV> RV> --------------------------------- RV> Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From w2agz at pacbell.net Sun May 11 05:12:06 2008 From: w2agz at pacbell.net (Paul M. Grant) Date: Sat, 10 May 2008 20:12:06 -0700 Subject: [Pw_forum] Charge Density Message-ID: <029001c8b314$cbc78eb0$6356ac10$@net> I've been assuming the units of charge density as stored in *.save and used in plotrho and accessed by xcrysden are scaled as (number of electrons/angstroms^3), but just thought I'd better check. Looking at the codes, examples and tutorials available for PWscf, I couldn't find any explicit confirmation (I'm sure there is somewhere) that this is indeed the case. I could try performing a volumetric integration on some simple example, but thought I'd ask the community first. It seems this is the case just by looking at the contours and surfaces produced by xcrysden, but I'm not too sure what the cryptic notation "delta n(r)" defines. I take it's the differential between isolevels in the units I've been using. Also, some time ago (about three months!), I switched from espresso-3.2.3 to o-sesame, and noticed that the charge density files in *.save are in a *.dat binary format rather than *.xml. What's going to be the future standard? Finally, and I think I asked about this before, is there a developers guide to the bowels of pw.x? The makefile links an enormous number of object files and I suppose one could figure this all out. Surely, there have been courses given at SISSA on its internal structure, if only in the shape of a flow chart. If these lectures are in Italian, no problem, and I would make a translation available to all. Ciao, -Paul Paul M. Grant, PhD Principal, W2AGZ Technologies Visiting Scholar, Applied Physics, Stanford University EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus w2agz at pacbell.net http://www.w2agz.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080510/10956c64/attachment.htm From bnrj.rudra at yahoo.com Sun May 11 06:33:36 2008 From: bnrj.rudra at yahoo.com (Rudra Banerjee) Date: Sun, 11 May 2008 10:03:36 +0530 (IST) Subject: [Pw_forum] slow relaxing Message-ID: <138197.95660.qm@web94108.mail.in2.yahoo.com> i am trying to do this PW calculation(water once again), but as you can see, the convergence ratio is very slow...is there any way to speed up the relaxation? 1 &CONTROL 2 calculation = 'relax' , 3 restart_mode = 'restart' , 4 outdir = '.' , 5 pseudo_dir = '/home/Rudra/espresso-3.2.3 /pseudo/' , 6 prefix = 'ring' , 7 etot_conv_thr = 1.0d-5 , 8 forc_conv_thr = 1.0d-4 , 9 nstep = 100 , 10 tstress = .true. , 11 tprnfor = .true. , 12 / 13 &SYSTEM 14 ibrav = 14, 15 celldm(1) = 35, 16 celldm(2) = 1, 17 celldm(3) = 1, 18 celldm(4) = 0, 19 celldm(5) = 0, 20 celldm(6) = 0, 21 nat = 18, 22 ntyp = 2, 23 ecutwfc = 60 , 24 / 25 &ELECTRONS 26 conv_thr = 1.0d-10 , 27 / 28 &IONS 29 ion_dynamics = 'bfgs' , 30 upscale = 30.D0 , 31 trust_radius_max = 5.0D-1 , 32 trust_radius_min = 1.0D-10, 33 / 34 ATOMIC_SPECIES 35 O 15.99000 O.BLYP.UPF 36 H 1.00000 H.fpmd.UPF 37 ATOMIC_POSITIONS bohr 38 O 0..452598E+01 0.199770E+01 -0.384251E+00 39 O -0.456645E+00 -0.494031E+01 0.587632E+00 40 O 0.417483E+01 -0.297334E+01 0.375756E+00 41 O -0.450000E+01 -0.199189E+01 0.492865E-01 42 O -0.413521E+01 0.302669E+01 -0.255022E-01 43 O 0.460540E+00 0.495314E+01 -0.751339E+00 44 H 0.565520E+01 0.257057E+01 0.950862E+00 45 H 0.433997E+01 0.115123E+00 -0.108584E+00 46 H -0.780642E+00 -0.583785E+01 0.216070E+01 47 H -0.195104E+01 -0.377112E+01 0.361755E+00 48 H 0.240252E+01 -0.368407E+01 0.466936E+00 49 H 0.500948E+01 -0.393069E+01 -0.955826E+00 50 H -0.432075E+01 -0.893828E-01 0.405553E-01 51 H -0.550895E+01 -0.239361E+01 -0.143549E+01 52 H -0.477693E+01 0.385892E+01 0.148439E+01 53 H -0.238065E+01 0.373511E+01 -0.293647E+00 54 H 0.196062E+01 0.377921E+01 -0.601195E+00 55 H 0.644296E+00 0.576927E+01 -0.238986E+01 56 57 K_POINTS automatic 58 3 3 3 1 1 1 ENERGY ----------- -205.1846032445 Ry -205.1846032445 Ry -205.1851434168 Ry -205..1859610477 Ry -205.1869410014 Ry -205.1873885307 Ry -205.1875891135 Ry -205.1878601381 Ry -205.1884629910 Ry -205.1886928104 Ry -205.1887148135 Ry -205.1889751236 Ry -205.1890151305 Ry -205.1890589222 Ry -205.1891438343 Ry -205.1892290624 Ry -205.1892951055 Ry -205.1894417283 Ry -205.1894831934 Ry -205.1895085510 Ry -205.1895218967 Ry -205.1895516832 Ry -205.1895640658 Ry -205.1895716262 Ry -205.1895746715 Ry -205.1895786741 Ry -205.1895832218 Ry -205.1895880554 Ry -205.1895927379 Ry -205.1895971238 Ry -205.1896015209 Ry -205.1896056880 Ry -- Rudra JRF; SNBNCBS http://www.bose.res.in/~rudra A bus station is where a bus stops. A train station is where a train stops. On my desk I have a work station. Please, if possible, don't send me MS Word or PowerPoint attachments Why?See: http://www.gnu.org/philosophy/no-word-attachments.html Best Jokes, Best Friends, Best Food and more. Go to http://in.promos.yahoo.com/groups/bestofyahoo/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080511/e3f8b439/attachment-0001.htm From baroni at sissa.it Sun May 11 09:36:27 2008 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 11 May 2008 09:36:27 +0200 Subject: [Pw_forum] Defining an antiferromagnetic graphene nanoribbon In-Reply-To: <765273.92348.qm@web33508.mail.mud.yahoo.com> References: <765273.92348.qm@web33508.mail.mud.yahoo.com> Message-ID: <0E4C5409-4CC6-4286-8895-889FAB4E996A@sissa.it> The kinetic-energy cutoff is a property of the atomic core, NOT of the specific system (to a large extent). SB On May 10, 2008, at 6:11 PM, Roberto G. A. Veiga wrote: > Dear Stefano: > > I'm using Ultrasoft PPs. My question was because this cutoff (20 Ry) > seemed to be appropriate for other carbonic systems. > > []s, > > Roberto > > Stefano Baroni wrote: > > On May 9, 2008, at 10:42 PM, Roberto G. A. Veiga wrote: > >> Hi, Konstantin: >> >> thank you very much. Such a large cutoff (80 Ry) is necessary for >> convergence? Or maybe I'm using one quite small (20 Ry)... > > it depends on the PP you are using, I guess, and certainly NOT on > the actual structure you are studying. 80 Ry seems like an > appropriate cutoff for moderately hard norm-conserving PP's, whereas > 20 Ry sounds like appriate for many US PP's. In either case, you > better check the aprporiateness by yourself, through thorough > convergence tests. > > Stefano > > >> >> >> []s, >> >> Roberto >> >> Konstantin Kudin wrote: >> Hi Roberto, >> >> Here is a ribbon input that works for sure: >> https://kiev.princeton.edu/misc/rg_07.scf.in >> (get PPs from the PWSCF website) >> >> Good luck! >> Kostya > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - > Trieste > [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une > morale de la pens?e - Jean Piaget > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > Be a better friend, newshound, and know-it-all with Yahoo! Mobile. > Try it now._______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080511/2d391ac5/attachment.htm From marzari at MIT.EDU Sun May 11 10:22:14 2008 From: marzari at MIT.EDU (Nicola Marzari) Date: Sun, 11 May 2008 11:22:14 +0300 Subject: [Pw_forum] slow relaxing In-Reply-To: <138197.95660.qm@web94108.mail.in2.yahoo.com> References: <138197.95660.qm@web94108.mail.in2.yahoo.com> Message-ID: <4826ACB6.1040403@mit.edu> hi Rudra, ideally, if you have 18 atoms, i.e. 56 degrees of freedom (or 53, if you remove traslations) a conjugate gradient algorithms should bring you to the minimum in 53 steps. You are not far away from that - you are using bfgs (not sure if there is an analytic results on the minimum number of moves). Also, restart probably remembers the approximate hessian (second derivative matrix) from the previous run, and that might not be that helpful, at the end, if you started away from equlibrium. Unless you are interested in empty states, or in ice, it's unlikely that using k-point sampling would be very interesting - I'd use gamma, and increase the sice of the cell. Last - you might want to play around with the parameters - it's a bit of a tricky issue, but basically what you need is that each ionic step the hellman-feynman forces need to be converged well enough for the ions to move in the right direction, but not too much. Why don't you take a smaller system, like a water trimer, in a supercell with gamma sampling, and try to work with etot_conv_thr and force_conv_thr and upscale until you converge to the tolerance you want in the least cpu time ? nicola Rudra Banerjee wrote: > i am trying to do this PW calculation(water once again), but as you can > see, the convergence ratio is very slow...is there any way to speed up > the relaxation? > > 1 &CONTROL > 2 calculation = 'relax' , > 3 restart_mode = 'restart' , > 4 outdir = '.' , > 5 pseudo_dir = '/home/Rudra/espresso-3.2.3 > /pseudo/' , > 6 prefix = 'ring' , > 7 etot_conv_thr = 1.0d-5 , > 8 forc_conv_thr = 1.0d-4 , > 9 nstep = 100 , > 10 tstress = .true. , > 11 tprnfor = .true. , > 12 / > 13 &SYSTEM > 14 ibrav = 14, > 15 celldm(1) = 35, > 16 celldm(2) = 1, > 17 celldm(3) = 1, > 18 celldm(4) = 0, > 19 celldm(5) = 0, > 20 celldm(6) = 0, > 21 nat = 18, > 22 ntyp = 2, > 23 ecutwfc = 60 , > 24 / > 25 &ELECTRONS > 26 conv_thr = 1.0d-10 , > 27 / > 28 &IONS > 29 ion_dynamics = 'bfgs' , > 30 upscale = 30.D0 , > 31 trust_radius_max = 5.0D-1 , > 32 trust_radius_min = 1.0D-10, > 33 / > 34 ATOMIC_SPECIES > 35 O 15.99000 O.BLYP.UPF > 36 H 1.00000 H.fpmd.UPF > 37 ATOMIC_POSITIONS bohr > 38 O 0.452598E+01 0.199770E+01 -0.384251E+00 > 39 O -0.456645E+00 -0.494031E+01 0.587632E+00 > 40 O 0.417483E+01 -0.297334E+01 0.375756E+00 > 41 O -0.450000E+01 -0.199189E+01 0.492865E-01 > 42 O -0.413521E+01 0.302669E+01 -0.255022E-01 > 43 O 0.460540E+00 0.495314E+01 -0.751339E+00 > 44 H 0.565520E+01 0.257057E+01 0.950862E+00 > 45 H 0.433997E+01 0.115123E+00 -0.108584E+00 > 46 H -0.780642E+00 -0.583785E+01 0.216070E+01 > 47 H -0.195104E+01 -0.377112E+01 0.361755E+00 > 48 H 0.240252E+01 -0.368407E+01 0.466936E+00 > 49 H 0.500948E+01 -0.393069E+01 -0.955826E+00 > 50 H -0.432075E+01 -0.893828E-01 0.405553E-01 > 51 H -0.550895E+01 -0.239361E+01 -0.143549E+01 > 52 H -0.477693E+01 0.385892E+01 0.148439E+01 > 53 H -0.238065E+01 0.373511E+01 -0.293647E+00 > 54 H 0.196062E+01 0.377921E+01 -0.601195E+00 > 55 H 0.644296E+00 0.576927E+01 -0.238986E+01 > 56 > 57 K_POINTS automatic > 58 3 3 3 1 1 1 > > > ENERGY > ----------- > > -205.1846032445 Ry > -205.1846032445 Ry > -205.1851434168 Ry > -205.1859610477 Ry > -205.1869410014 Ry > -205.1873885307 Ry > -205.1875891135 Ry > -205.1878601381 Ry > -205.1884629910 Ry > -205.1886928104 Ry > -205.1887148135 Ry > -205.1889751236 Ry > -205.1890151305 Ry > -205..1890589222 Ry > -205.1891438343 Ry > -205.1892290624 Ry > -205.1892951055 Ry > -205.1894417283 Ry > -205.1894831934 Ry > -205.1895085510 Ry > -205.1895218967 Ry > -205.1895516832 Ry > -205.1895640658 Ry > -205.1895716262 Ry > -205.1895746715 Ry > -205.1895786741 Ry > -205.1895832218 Ry > -205.1895880554 Ry > -205.1895927379 Ry > -205.1895971238 Ry > -205.1896015209 Ry > -205.1896056880 Ry > > -- > Rudra > JRF; SNBNCBS > http://www.bose.res.in/~rudra > > > A bus station is where a bus stops. A train station is where a train > stops. On my desk I have a work station. > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why?See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > ------------------------------------------------------------------------ > Meet people who discuss and share your passions. Join them now. > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From paulatto at sissa.it Sun May 11 11:59:05 2008 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Sun, 11 May 2008 11:59:05 +0200 (CEST) Subject: [Pw_forum] Charge Density In-Reply-To: <029001c8b314$cbc78eb0$6356ac10$@net> References: <029001c8b314$cbc78eb0$6356ac10$@net> Message-ID: <15008.79.16.237.50.1210499945.squirrel@webmail.sissa.it> On Sun, May 11, 2008 05:12, Paul M. Grant wrote: > in plotrho and accessed by xcrysden are scaled as (number of > electrons/angstroms^3), but just thought I'd better check. Dear Paul, internally the charge density is normalized to the number of electrons (the code tells it at the beginning: starting charge X, renormalised to Y). There could be some problem because internal units are bohr, while xcd uses angs, in any case the sum of the charge density on a grid of equally spaced points must yield the number of electrons. > What's going to be the future standard? I'm not sure, but I think only the suffix changed. > Finally, and I think I asked about this before, is there a developers > guide to the bowels of pw.x? I fear there is no such guide, the core of the code is in electrons.f90, which is called from pwscf.f90. Most of the files are extremely technical and doesn't have to be understood. Anyway, I think such a guide could be very useful, but I can't think of anybody to write it. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) +39 040 3787 511 http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From raveiga at yahoo.com Sun May 11 14:35:53 2008 From: raveiga at yahoo.com (Roberto G. A. Veiga) Date: Sun, 11 May 2008 05:35:53 -0700 (PDT) Subject: [Pw_forum] Defining an antiferromagnetic graphene nanoribbon In-Reply-To: <0E4C5409-4CC6-4286-8895-889FAB4E996A@sissa.it> Message-ID: <784495.47590.qm@web33502.mail.mud.yahoo.com> Hi, Stefano: as far as I understand, if I use a cutoff for a system made of carbons and I find it is appropriate, I should use the same cutoff for another system also made of carbons. I mean, if I use 20 Ry for carbon nanotubes and the results are fine, I could use 20 Ry for diamond, or graphene. Is it wrong my assumption? []s, Roberto Stefano Baroni wrote: The kinetic-energy cutoff is a property of the atomic core, NOT of the specific system (to a large extent).SB On May 10, 2008, at 6:11 PM, Roberto G. A. Veiga wrote: Dear Stefano: I'm using Ultrasoft PPs. My question was because this cutoff (20 Ry) seemed to be appropriate for other carbonic systems. []s, Roberto Stefano Baroni wrote: On May 9, 2008, at 10:42 PM, Roberto G. A. Veiga wrote: Hi, Konstantin: thank you very much. Such a large cutoff (80 Ry) is necessary for convergence? Or maybe I'm using one quite small (20 Ry)... it depends on the PP you are using, I guess, and certainly NOT on the actual structure you are studying. 80 Ry seems like an appropriate cutoff for moderately hard norm-conserving PP's, whereas 20 Ry sounds like appriate for many US PP's. In either case, you better check the aprporiateness by yourself, through thorough convergence tests. Stefano []s, Roberto Konstantin Kudin wrote: Hi Roberto, Here is a ribbon input that works for sure: https://kiev.princeton.edu/misc/rg_07.scf.in (get PPs from the PWSCF website) Good luck! Kostya --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum --------------------------------- Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now._______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum --------------------------------- Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080511/9e348d09/attachment-0001.htm From hande at newton.physics.metu.edu.tr Sun May 11 14:51:55 2008 From: hande at newton.physics.metu.edu.tr (Hande Ustunel) Date: Sun, 11 May 2008 15:51:55 +0300 (EEST) Subject: [Pw_forum] Defining an antiferromagnetic graphene nanoribbon In-Reply-To: <784495.47590.qm@web33502.mail.mud.yahoo.com> Message-ID: Dear Roberto, If I may jump in, I don't suppose it would be terribly costly to repeat one of your calculations with a cutoff that is slightly higher once you are done with the lower cutoff. You can compare whichever quantities you are interested in between the two cutoffs and decide whether the error is within a threshold that is self-determined/acceptable by the community at large. This would verify once and for all the appropriateness of your cutoff. Keep in mind however that for a system such as a graphene ribbon the cutoff may not be the only parameter to optimize. There's still the smearing and the amount of vaccum to worry about. For this reason, you should consider an isolated preliminary cutoff convergence study in a simpler system such as diamond or better still graphene as suggested in previous replies to your post. Best wishes, Hande On Sun, 11 May 2008, Roberto G. A. Veiga wrote: > Hi, Stefano: > > as far as I understand, if I use a cutoff for a system made of carbons and I find it is appropriate, I should use the same cutoff for another system also made of carbons. I mean, if I use 20 Ry for carbon nanotubes and the results are fine, I could use 20 Ry for diamond, or graphene. Is it wrong my assumption? > > []s, > > Roberto > > Stefano Baroni wrote: The kinetic-energy cutoff is a property of the atomic core, NOT of the specific system (to a large extent).SB > > On May 10, 2008, at 6:11 PM, Roberto G. A. Veiga wrote: > > Dear Stefano: > > I'm using Ultrasoft PPs. My question was because this cutoff (20 Ry) seemed to be appropriate for other carbonic systems. > > []s, > > Roberto > > Stefano Baroni wrote: > On May 9, 2008, at 10:42 PM, Roberto G. A. Veiga wrote: > > Hi, Konstantin: > > thank you very much. Such a large cutoff (80 Ry) is necessary for convergence? Or maybe I'm using one quite small (20 Ry)... > > it depends on the PP you are using, I guess, and certainly NOT on the actual structure you are studying. 80 Ry seems like an appropriate cutoff for moderately hard norm-conserving PP's, whereas 20 Ry sounds like appriate for many US PP's. In either case, you better check the aprporiateness by yourself, through thorough convergence tests. > > > Stefano > > > > > > []s, > > Roberto > > Konstantin Kudin wrote: Hi Roberto, > > Here is a ribbon input that works for sure: > https://kiev.princeton.edu/misc/rg_07.scf.in > (get PPs from the PWSCF website) > > Good luck! > Kostya > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste > [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) > > > La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget > > > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > --------------------------------- > Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now._______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste > [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) > > > La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget > > > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > --------------------------------- > Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. -- Hande Ustunel Department of Physics Office 439 Middle East Technical University Ankara 06531, Turkey Tel : +90 312 210 3264 http://www.physics.metu.edu.tr/~hande From marzari at MIT.EDU Sun May 11 15:49:52 2008 From: marzari at MIT.EDU (Nicola Marzari) Date: Sun, 11 May 2008 09:49:52 -0400 Subject: [Pw_forum] Defining an antiferromagnetic graphene nanoribbon In-Reply-To: <784495.47590.qm@web33502.mail.mud.yahoo.com> References: <784495.47590.qm@web33502.mail.mud.yahoo.com> Message-ID: <4826F980.7060103@mit.edu> Roberto G. A. Veiga wrote: > Hi, Stefano: > > as far as I understand, if I use a cutoff for a system made of carbons > and I find it is appropriate, I should use the same cutoff for another > system also made of carbons. I mean, if I use 20 Ry for carbon nanotubes > and the results are fine, I could use 20 Ry for diamond, or graphene. Is > it wrong my assumption? The convergence tests for ultrasoft carbon are actually posted on the webpage: http://www.quantum-espresso.org/pseudo/upfdetails.php?upf=C.pbe-rrkjus.UPF Interesting, sp2 carbon (graphite) looks a bit smoother than sp3 carbon (diamond) (I do wonder why) but roughly the cutoffs are the same. nicola -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From baroni at sissa.it Sun May 11 18:55:04 2008 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 11 May 2008 18:55:04 +0200 Subject: [Pw_forum] slow relaxing In-Reply-To: <4826ACB6.1040403@mit.edu> References: <138197.95660.qm@web94108.mail.in2.yahoo.com> <4826ACB6.1040403@mit.edu> Message-ID: a few remarks for the benefit of the less experienced members of the forum: On May 11, 2008, at 10:22 AM, Nicola Marzari wrote: > ideally, if you have 18 atoms, i.e. 56 degrees of freedom (or 53, if > you > remove traslations) a conjugate gradient algorithms should bring you > to > the minimum in 53 steps. this is strictly true for a quadratic function. a non quadratic one may require more iterations. also, the number of degrees of freedon should be considered as an upper bound for the number of iterations needed to minimize a quadratic functional using CG's. this upper limit is only reached for very ill-conditioned functionals (those whose quadratic form has eigenvalues of wildly different order of magnitude). well conditioned functionals (whose quadratic form has eigenvalues all of about the same magnitude) usually converge much faster. to some extent, the above two facts (non quadraticity, better condition of the quadratic form) and may compensate, I guess. Stefano --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080511/dbd10dca/attachment.htm From akohlmey at cmm.chem.upenn.edu Sun May 11 18:43:38 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sun, 11 May 2008 12:43:38 -0400 (EDT) Subject: [Pw_forum] slow relaxing In-Reply-To: References: <138197.95660.qm@web94108.mail.in2.yahoo.com> <4826ACB6.1040403@mit.edu> Message-ID: On Sun, 11 May 2008, Stefano Baroni wrote: perhaps one more comment on top of that mentioning a subject that is easily forgotten. i noticed that in the example input the wavefunction cutoff was chosen somewhat low (if not too low at 60ry) for norm-conserving pseudopotentials on an oxygen containing system. with a low (density) cutoff there will be a residual "ripples" on the density since you are missing high frequency components. as a consequence the minimum your system "sees" may actually change with the displacement of atoms or the whole system. this artefact will of course interfere with the geometry convergence behavior, particularly for gradient corrected functionals, and particularly for systems where you have "vacuum" areas in which those oscillations will have the largest relative impact. in part the latter effect is handled by a cutoff to not compute XC functionals if the densities, but it still is an effect to consider. in conclusion, the more tightly you want to converge your geometry, the higher cutoff you need. one has to keep in mind, though, that there are also the systematic errors of DFT to be considered and that it is of little use to converge geometries (far) beyond. cheers, axel. SB> a few remarks for the benefit of the less experienced members of the forum: SB> SB> On May 11, 2008, at 10:22 AM, Nicola Marzari wrote: SB> SB> >ideally, if you have 18 atoms, i.e. 56 degrees of freedom (or 53, if you SB> >remove traslations) a conjugate gradient algorithms should bring you to SB> >the minimum in 53 steps. SB> SB> this is strictly true for a quadratic function. a non quadratic one may SB> require more iterations. SB> SB> also, the number of degrees of freedon should be considered as an upper SB> bound for the number of iterations needed to minimize a quadratic functional SB> using CG's. this upper limit is only reached for very ill-conditioned SB> functionals (those whose quadratic form has eigenvalues of wildly different SB> order of magnitude). well conditioned functionals (whose quadratic form has SB> eigenvalues all of about the same magnitude) usually converge much faster. SB> SB> to some extent, the above two facts (non quadraticity, better condition of SB> the quadratic form) and may compensate, I guess. SB> SB> Stefano SB> SB> --- SB> Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste SB> [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) SB> SB> La morale est une logique de l'action comme la logique est une morale de la SB> pens?e - Jean Piaget SB> SB> Please, if possible, don't send me MS Word or PowerPoint attachments SB> Why? See: http://www.gnu.org/philosophy/no-word-attachments.html SB> SB> SB> SB> SB> SB> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From baroni at sissa.it Sun May 11 19:16:05 2008 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 11 May 2008 19:16:05 +0200 Subject: [Pw_forum] Defining an antiferromagnetic graphene nanoribbon In-Reply-To: <4826F980.7060103@mit.edu> References: <784495.47590.qm@web33502.mail.mud.yahoo.com> <4826F980.7060103@mit.edu> Message-ID: On May 11, 2008, at 3:49 PM, Nicola Marzari wrote: > The convergence tests for ultrasoft carbon are actually posted on the > webpage: > > http://www.quantum-espresso.org/pseudo/upfdetails.php?upf=C.pbe-rrkjus.UPF > > Interesting, sp2 carbon (graphite) looks a bit smoother than > sp3 carbon (diamond) (I do wonder why) but roughly the cutoffs > are the same. The energy gain in going form one cutoff to the next is very similar in the two plots, reflecting the same effective number of p electrons in graphite and carbon. If this number was different, I would expect the energy difference between two cutoffs to depend on the structure, because the s-channel potential should be softer than the p-channel one. For instance, I would expect the energy per atom in diamond to behave similarly as for an isolated atom in a sp3 configuration, but differently from an s2p2 atom (the energy of the latter should depend less on the cutoff). This is just a guess. Has anybody evidence of this? In the specific case, the main difference between the convergence tests reported for diamond and graphite is not the absolute convergence, which is quite similar in the two cases, but rather that, for lower cutoffs, the E-vs-V curve looks more rugged for diamond than for graphite. Couldn't this be simply a consequence of the smaller number of k-points used for the former than for the latter? Discontinuities in the E-vs-V curve are due to the sudden increase in the number plane waves when the cutoff crosses some critical values (when an infinitesimal increase of the volume of the reciprocal-space sphere of radius \sqrt{ecut} lets one or more G vectors be included in the sphere). This critical values depend on the k-point around which the sphere is centered. Using more k-points usually has a compensating effect on the discontinuities. That's why the more the k-points, the less rugged the E-vs.V curves usually look. Of course, this does not indicate that the convergence is faster the larger the number of k- points, but only that the E-vs-V smoothness, by itself, is not a good indicator of cutoff convergence. Am I wrong? Stefano --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080511/cabd9cbc/attachment-0001.htm From marzari at MIT.EDU Sun May 11 19:46:27 2008 From: marzari at MIT.EDU (Nicola Marzari) Date: Sun, 11 May 2008 13:46:27 -0400 Subject: [Pw_forum] Defining an antiferromagnetic graphene nanoribbon In-Reply-To: References: <784495.47590.qm@web33502.mail.mud.yahoo.com> <4826F980.7060103@mit.edu> Message-ID: <482730F3.3030103@mit.edu> Thanks Stefano for the feedback on the different issues ! On the first part (sp3 and sp2+pz having the same number of effective electrons in the p and s channels) I would tend to agree - but it would be indeed nice to do an experiment with a carbon atom having occupation numbers 2 2/3 2/3 2/3, and 1 1 1 1 for the 4 levels (2s and 2p) - energy as a function of cutoff. The second case should be closer to diamond and graphite/graphene than the first. Any takers ? On the second part, I'm a bit more puzzled. I agree that discontinuities in the E-vs-V curve appear, especially for sparse k-point sampling, due to the sudden increase in the number plane waves when the cutoff crosses some critical value. Still, those discontinuities would always appear as a sudden drop in total energy, since the basis of plane waves has discontinuously become larger. http://www.pwscf.org/pseudo/1.3/UPF/C.pbe-rrkjus-test-diamond.pdf looked a bit different - hence my puzzlement. I though at augmentation charges and the existence of fourier oscillations outside the core region, due to the multipole representation of the charge, but not sure why it would be more relevant in diamond (where the C-C distance is longer) nicola --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From giannozz at nest.sns.it Sun May 11 20:02:02 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Sun, 11 May 2008 20:02:02 +0200 Subject: [Pw_forum] Charge Density In-Reply-To: <029001c8b314$cbc78eb0$6356ac10$@net> References: <029001c8b314$cbc78eb0$6356ac10$@net> Message-ID: <3CAA2E39-884B-41E1-A354-4E2AFFB12141@nest.sns.it> On May 11, 2008, at 5:12 , Paul M. Grant wrote: > I?ve been assuming the units of charge density as stored in *.save > and used in plotrho and accessed by xcrysden are scaled as (number > of electrons/angstroms^3) > number of electrons/(a.u.)^3 is a better assumption (no warranty). PWscf uses atomic (Rydberg) units everywhere, unless explicitly specified. In order to preserve genetic diversity, guess what? CP uses Hartree atomic units. > Also, some time ago (about three months!), I switched from > espresso-3.2.3 to o-sesame > you mean: the development version in the cvs repository, that for historical reasons has 'o-sesame' as root directory? > and noticed that the charge density files in *.save are in a *.dat > binary format rather than *.xml. What?s going to be the future > standard? > it was done to fix some inconsistencies in the naming convention: http://www.democritos.it:8888/O-sesame/chngview?cn=5687 See also the following for recent changes of the file format: http://www.democritos.it:8888/O-sesame/chngview?cn=5744 http://www.democritos.it:8888/O-sesame/chngview?cn=5795 It is unfortunate that the file format had to be changed (once again) at this stage, but these should hopefully be the last major changes that can affect other people's software reading those files, if any exists (Q-E will keep reading old files). > Finally, and I think I asked about this before, is there a > developers guide to the bowels of pw.x? The makefile links an > enormous number of object files and I suppose one could figure this > all out. > the closest thing to a developer's guide is, well, the "developer manual" linked in the main page of the wiki: http://www.quantum-espresso.org/wiki/index.php/Developer_Manual It used to be available as a latex file in previous versions. I wrote it as a template some time ago and from time to time I add to it some piece of information that I deem suitable. One can find there a few important things like the specifications of the file format, but what is missing vastly exceeds what is present. Documentation of what a single *.f90 does is not supposed to be written in the guide, though, but in each file. Sometimes there is something useful (although in an unstructured way), sometimes there is nothing useful, depending on the mood of the developer. There are no flow charts of anything. If anybody knows any simple automated way (e.g. by transforming code into linkable html) to locate calls, variables in modules, etc, it would be very useful. Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From akohlmey at cmm.chem.upenn.edu Sun May 11 20:19:21 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sun, 11 May 2008 14:19:21 -0400 (EDT) Subject: [Pw_forum] Charge Density In-Reply-To: <3CAA2E39-884B-41E1-A354-4E2AFFB12141@nest.sns.it> References: <029001c8b314$cbc78eb0$6356ac10$@net> <3CAA2E39-884B-41E1-A354-4E2AFFB12141@nest.sns.it> Message-ID: On Sun, 11 May 2008, Paolo Giannozzi wrote: hi paolo, [...] PG> Documentation of what a single *.f90 does is not supposed to be PG> written in the guide, though, but in each file. Sometimes there is PG> something useful (although in an unstructured way), sometimes PG> there is nothing useful, depending on the mood of the developer. ...which largely reflects the way software development works these days in academic environments. there are no credits to be had for writing something in a way that it can serve as a foundation for future projects or so that it fits well into the existing code. you only get credit for getting it done (through the publications). there is nobody around to teach how to program well, altogether and for a large package program in particular. one has to be happy if people know a programming language well enough to get the job done. just take a survey of how many people these days ask "is there a feature XXX, and if not can somebody please implement it?" instead of "where should i start to implement XXX?". the fact that a correlated and concerted effort to improve the overall code interoperability and consistency will help _much_ more in the long run is frequently ignored. this is what is so great about the Q-E effort, that there _is_ backing for going those extra steps and that there _are_ people willing to do this, and the improvements in the code over time are proof for it. one cannot regard this high enough, because for the reasons from above, this ususally comes at the expense of limiting ones own carreer. PG> There are no flow charts of anything. If anybody knows any simple PG> automated way (e.g. by transforming code into linkable html) to PG> locate calls, variables in modules, etc, it would be very useful. the latest version of doxygen has fortran 90/95 support (cp2k uses it), that would also allow to place coded comments into the code to associate functions and modules with (short) descriptions which can be seen from the overview pages (and lots of html stuff...). it looks a bit odd, since doxygen was written for C++. there also is a python script the thierry deutsch wrote looooong ago for CPMD. it does a pretty good job, but would need some adjustments. i'm certain that thierry would give his blessing if somebody adapts it to work with QE. are there any python hackers around that need a challenge? :-) cheers, axel. PG> PG> Paolo PG> --- PG> Paolo Giannozzi, Dept of Physics, University of Udine PG> via delle Scienze 208, 33100 Udine, Italy PG> Phone +39-0432-558216, fax +39-0432-558222 PG> PG> PG> PG> _______________________________________________ PG> Pw_forum mailing list PG> Pw_forum at pwscf.org PG> http://www.democritos.it/mailman/listinfo/pw_forum PG> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From degironc at sissa.it Mon May 12 09:43:26 2008 From: degironc at sissa.it (Stefano de Gironcoli) Date: Mon, 12 May 2008 09:43:26 +0200 Subject: [Pw_forum] Defining an antiferromagnetic graphene nanoribbon In-Reply-To: <482730F3.3030103@mit.edu> References: <784495.47590.qm@web33502.mail.mud.yahoo.com> <4826F980.7060103@mit.edu> <482730F3.3030103@mit.edu> Message-ID: <4827F51E.3030205@sissa.it> Hi Nicola, I think that graphite curves in your tests appear smoother that the diamonds one because the 664 grid used for G is denser than the 444 used in D. Increasing the cutoff smooths the curves because the sudden jumps become smaller as the basis gets more complete. But E-vs-V becomes also smoother when the k-point sampling is increased because each sampled k-point will determine a jump at a different volume (weighted by 1/Nk) so that for denser grids there are more, smaller jumps hence smoother curves. Ideally if one were integrating over the full BZ (something impossible to do but conceptually useful to establish the trend) the E-vs-V curve would be completely smooth because the PW basis would be independent on the volume: only the assignment of a particular basis function to a particular k-point would change with the structure but the overall basis would be exactly the same. stefano Nicola Marzari wrote: > On the second part, I'm a bit more puzzled. I agree that > discontinuities in the E-vs-V curve appear, especially for > sparse k-point sampling, due to the sudden increase in > the number plane waves when the cutoff crosses some critical > value. Still, those discontinuities would always appear as a > sudden drop in total energy, since the basis of plane waves has > discontinuously become larger. > http://www.pwscf.org/pseudo/1.3/UPF/C.pbe-rrkjus-test-diamond.pdf > looked a bit different - hence my puzzlement. I though at augmentation > charges and the existence of fourier oscillations outside the core > region, due to the multipole representation of the charge, but > not sure why it would be more relevant in diamond (where the C-C > distance is longer) From limkr at umich.edu Mon May 12 22:17:24 2008 From: limkr at umich.edu (Dong-Hee Lim) Date: Mon, 12 May 2008 16:17:24 -0400 Subject: [Pw_forum] QE run example 02 Message-ID: <20080512161724.19673qlpixgspry8@web.mail.umich.edu> Dear PWscf users I was wondering if there was any error in the QE run example 02. It is about the frequency calculation. Among the calculations shown in the example 02, I could get the same results of the scf calculations as shown in the reference data, but I can't get any results of phonon calculation at Gamma and at X like as following; phonons of Si at Gamma &inputph tr2_ph=1.0d-14, prefix='si', epsil=.true., amass(1)=28.08, outdir='$TMP_DIR/', fildyn='si.dynG', / 0.0 0.0 0.0 Although I have tried many times to get any results from the example 02 file, I can't get anything.. I would appreciate if you checked that there was any error in the example 02. Thank you, Dong-Hee Lim From polynmr at physics.unc.edu Mon May 12 22:54:17 2008 From: polynmr at physics.unc.edu (Charles Chen) Date: Mon, 12 May 2008 16:54:17 -0400 Subject: [Pw_forum] QE run example 02 In-Reply-To: <20080512161724.19673qlpixgspry8@web.mail.umich.edu> References: <20080512161724.19673qlpixgspry8@web.mail.umich.edu> Message-ID: <4828AE79.1080905@physics.unc.edu> You sure you have the TMP_DIR correctly set? what's the error message? Dong-Hee Lim wrote: > Dear PWscf users > > I was wondering if there was any error in the QE run example 02. > It is about the frequency calculation. > Among the calculations shown in the example 02, I could get the same > results of the scf calculations as shown in the reference data, but I > can't get any results of phonon calculation at Gamma and at X like as > following; > > phonons of Si at Gamma > &inputph > tr2_ph=1.0d-14, > prefix='si', > epsil=.true., > amass(1)=28.08, > outdir='$TMP_DIR/', > fildyn='si.dynG', > / > > 0.0 0.0 0.0 > what is this line? Do you miss something here? > Although I have tried many times to get any results from the example > 02 file, I can't get anything.. > > I would appreciate if you checked that there was any error in the example 02. > > Thank you, > Dong-Hee Lim > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > Charles -- NMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMR NMR Dr. Qiang "Charles" Chen NMR NMR Department of Physics and Astronomy NMR NMR University of North Carolina NMR NMR Phillips Hall, CB#3255 NMR NMR Chapel Hill, NC 27599-3255 NMR NMR Tel: 919-962-1571 (O) NMR NMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMRNMR From giannozz at nest.sns.it Tue May 13 07:55:05 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 13 May 2008 07:55:05 +0200 Subject: [Pw_forum] QE run example 02 In-Reply-To: <20080512161724.19673qlpixgspry8@web.mail.umich.edu> References: <20080512161724.19673qlpixgspry8@web.mail.umich.edu> Message-ID: <48292D39.505@nest.sns.it> Dong-Hee Lim wrote: > I would appreciate if you checked that there was any error in the example 02. I would appreciate that you check whether you correctly run example 02 -- Paolo Giannozzi, Democritos and University of Udine, Italy From sagarambavale at yahoo.co.in Tue May 13 08:31:16 2008 From: sagarambavale at yahoo.co.in (ambavale sagar) Date: Tue, 13 May 2008 12:01:16 +0530 (IST) Subject: [Pw_forum] acml - mkl Message-ID: <352219.76309.qm@web94610.mail.in2.yahoo.com> Dear Pwscf users, I have x86_64 (i.e. AMD64) architacture machine with Xeon (x5450-quad core) processors having dual cpu. I have installed intel fortran compiler, c compiler and mkl. But as i compile espresso4cvs2 version it does not recognise BLAS,LAPACK libraries. Must i install ACML as i have AMD architacture? During compilation of acml i couldn't find driver.f( They say that driver.f is application program). What should be the procedure? One more question: Is it possible to have Xeon processors with ia-64 architacture? regards Sagar Ambavale Research Student The M.S.University of Baroda India Best Jokes, Best Friends, Best Food and more. Go to http://in.promos.yahoo.com/groups/bestofyahoo/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080513/cb7c613b/attachment.htm From giannozz at nest.sns.it Tue May 13 10:17:18 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 13 May 2008 10:17:18 +0200 Subject: [Pw_forum] acml - mkl In-Reply-To: <352219.76309.qm@web94610.mail.in2.yahoo.com> References: <352219.76309.qm@web94610.mail.in2.yahoo.com> Message-ID: <48294E8E.5010409@nest.sns.it> ambavale sagar wrote: > I have x86_64 (i.e. AMD64) architacture machine with Xeon (x5450-quad > core) processors having dual cpu. x86_64 can be both AMD and INtel; Xeon is Intel, not AMD. -- Paolo Giannozzi, Democritos and University of Udine, Italy From akohlmey at cmm.chem.upenn.edu Tue May 13 12:09:20 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 13 May 2008 06:09:20 -0400 (EDT) Subject: [Pw_forum] acml - mkl In-Reply-To: <352219.76309.qm@web94610.mail.in2.yahoo.com> References: <352219.76309.qm@web94610.mail.in2.yahoo.com> Message-ID: On Tue, 13 May 2008, ambavale sagar wrote: AS> Dear Pwscf users, AS> I have x86_64 (i.e. AMD64) architacture machine with Xeon AS> (x5450-quad core) processors having dual cpu. I have installed intel AS> fortran compiler, c compiler and mkl. But as i compile espresso4cvs2 AS> version it does not recognise BLAS,LAPACK libraries. Must i install if configure does not find MKL, it either means you have not installed it correctly or to a location that configure does not know about. check the config.log file and simply adapt the make.sys file manually according to the MKL user's guide (RTFM!!). AS> ACML as i have AMD architacture? During compilation of acml i both the 64-bit ACML and MKL should in principle work interchangably. one would expect ACML to work better on AMD cpus and MKL on intel, but in real life that varies. AS> couldn't find driver.f( They say that driver.f is application AS> program). What should be the procedure? you didn't read the documentation correctly. ACML does not need to be compiled. this obviously explains how to compile an example application to use ACML. since QE uses the standard BLAS/LAPACK calls you only have to adapt the respective entries in make.sys it even has comments to explain. if you have installed MKL (version 10.x) correctly a simple -lmkl would do for BLAS (and automatically LAPACK) in case of a serial compile. if you want to compile a parallel version, things get more complicated. please see the multitude of previous discussions on this subject in the mailing list archive. SA> One more question: Is it possible to have Xeon processors with ia-64 SA> architacture? this is impossible. IA64 is itanium. cheers, axel. regards Sagar Ambavale Research Student The M.S.University of Baroda India Best Jokes, Best Friends, Best Food and more. Go to http://in.promos.yahoo.com/groups/bestofyahoo/ -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From gaoguoying at gmail.com Wed May 14 05:10:04 2008 From: gaoguoying at gmail.com (Guoying Gao) Date: Wed, 14 May 2008 11:10:04 +0800 Subject: [Pw_forum] question on pseudopotential Message-ID: <6234c0c60805132010h52e43817sf7177be6e6aa664d@mail.gmail.com> Dear everyone, I downloaded the pseudopotential from www.abinit.org with the format of x.fhi file. After that, I transformed it to the requested format of Quantum-espresso code. However, how could I know the cutoff radius of the atom? Is there anyone know about this? Any suggestion will be welcomed. Guoying Gao National Lab of superhard materials Jilin University China From giannozz at nest.sns.it Wed May 14 13:56:09 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 14 May 2008 13:56:09 +0200 Subject: [Pw_forum] question on pseudopotential In-Reply-To: <6234c0c60805132010h52e43817sf7177be6e6aa664d@mail.gmail.com> References: <6234c0c60805132010h52e43817sf7177be6e6aa664d@mail.gmail.com> Message-ID: <482AD359.2000603@nest.sns.it> Guoying Gao wrote: > However, how could I know the cutoff radius of the atom? if it is not written in the original file (and I think it isn't) or in some reference paper, the only possibility is to ask whoever generated it, if known Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From zx3 at rice.edu Wed May 14 18:47:36 2008 From: zx3 at rice.edu (zx3 at rice.edu) Date: Wed, 14 May 2008 11:47:36 -0500 Subject: [Pw_forum] eigenvalue ordering in bands structure calculation Message-ID: <1210783656.482b17a80e452@webmail.mail.rice.edu> Dear all: During calculating band structure of a zigzag band structure which has partial flat band at the fermi level, I found that at some k points, the eigenvalues written by bands.x are not ordered from lower to higher, it introduces problems when I plot using gnuplot. I can modify band_plot.f90 to reorder this, but I wonder where is the origin of this problem, and whether it will give wrong results in further process, such as transport calculation. Thanks. some of the parameters are: &system nspin = 1, ecutwfc = 30.0, ecutrho = 240.0 occupations='smearing', smearing='gaussian', degauss=0.03, nbnd = 50, / &electrons conv_thr = 1.0e-10, mixing_beta = 0.3, diagonalization = 'cg', / the full input file can be found at http://www.ruf.rice.edu/~zx3/ribbon.nscf Best, Zhiping From giannozz at nest.sns.it Wed May 14 20:45:24 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 14 May 2008 20:45:24 +0200 Subject: [Pw_forum] eigenvalue ordering in bands structure calculation In-Reply-To: <1210783656.482b17a80e452@webmail.mail.rice.edu> References: <1210783656.482b17a80e452@webmail.mail.rice.edu> Message-ID: <71D47969-EEEA-4CBF-A469-2BA684BA444A@nest.sns.it> On May 14, 2008, at 18:47 , zx3 at rice.edu wrote: > During calculating band structure of a zigzag band structure which has > partial flat band at the fermi level, I found that at some k > points, the > eigenvalues written by bands.x are not ordered from lower to > higher, it > introduces problems when I plot using gnuplot. > I can modify band_plot.f90 to reorder this, but I wonder where > is the origin > of this problem it doesn't work as one would like, but it works as promised. In PP/ bands.f90: !----------------------------------------------------------------------- SUBROUTINE punch_band (filband, spin_component, lsigma, no_overlap) !-------------------------------------------------------------------- --- ! ! This routine writes the band energies on a file. The routine orders ! the eigenvalues using the overlap of the eigenvectors to give ! an estimate crossing and anticrossing of the bands. This simplified ! method works in many, but not in all the cases. Notice the last sentence! Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From yahyaei99 at yahoo.com Thu May 15 07:06:49 2008 From: yahyaei99 at yahoo.com (hamad mohamed) Date: Wed, 14 May 2008 22:06:49 -0700 (PDT) Subject: [Pw_forum] (no subject) Message-ID: <460980.91975.qm@web82002.mail.mud.yahoo.com> Dear Users and Developers error message %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% cannot remap grid on k-point list %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% is a peering by performing the electron phonon coupling for a tetragonal body center unit cell, where the meshes are: dense 24 24 24 0 0 0 rare 2 2 2 0 0 0 phonon 2 2 1 where all the division of nk and nq that correspond to dense/rare , dense/phonon and rare/phonon are integer. on the other hand the phonon calculation by it self is working with out any error for the non-spin polarized case and with out the LDA+U too. All suggestions are welcome. Thanks a lot regards H.M.Alyahyaei California State University Los Angeles Physics and Astronomy Department -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080514/86a9945a/attachment.htm From yahyaei99 at yahoo.com Thu May 15 07:09:13 2008 From: yahyaei99 at yahoo.com (hamad mohamed) Date: Wed, 14 May 2008 22:09:13 -0700 (PDT) Subject: [Pw_forum] electron phonon coupling / cannot remap grid on k-point list error Message-ID: <899166.36606.qm@web82003.mail.mud.yahoo.com> Dear pwscf Users and Developers error message %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% cannot remap grid on k-point list %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% is a peering by performing the electron phonon coupling for a tetragonal body center unit cell, where the meshes are: dense 24 24 24 0 0 0 rare 2 2 2 0 0 0 phonon 2 2 1 where all the division of nk and nq that correspond to dense/rare , dense/phonon and rare/phonon are integer. on the other hand the phonon calculation by it self is working with out any error for the non-spin polarized case and with out the LDA+U too. All suggestions are welcome. Thanks a lot regards H.M.Alyahyaei California State University Los Angeles Physics and Astronomy Department -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080514/6a2103fd/attachment.htm From bnrj.rudra at yahoo.com Thu May 15 13:54:02 2008 From: bnrj.rudra at yahoo.com (Rudra Banerjee) Date: Thu, 15 May 2008 17:24:02 +0530 (IST) Subject: [Pw_forum] print time Message-ID: <251184.10075.qm@web94113.mail.in2.yahoo.com> Dear developers, can you plz provide me a stand alone version of print_time_pw ? Regards, -- Rudra JRF; SNBNCBS http://www.bose.res.in/~rudra A bus station is where a bus stops. A train station is where a train stops. On my desk I have a work station. Please, if possible, don't send me MS Word or PowerPoint attachments Why?See: http://www.gnu.org/philosophy/no-word-attachments.html Bring your gang together. Do your thing. Find your favourite Yahoo! group at http://in.promos.yahoo.com/groups/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080515/15219bc7/attachment.htm From giannozz at nest.sns.it Thu May 15 14:11:28 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 15 May 2008 14:11:28 +0200 Subject: [Pw_forum] print time In-Reply-To: <251184.10075.qm@web94113.mail.in2.yahoo.com> References: <251184.10075.qm@web94113.mail.in2.yahoo.com> Message-ID: <482C2870.5030207@nest.sns.it> Rudra Banerjee wrote: > Dear developers, > can you plz provide me a stand alone version of print_time_pw ? there is no such thing as "print_time_pw": $ grep -i print_time_pw */*f90 $ Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From bnrj.rudra at yahoo.com Thu May 15 14:50:58 2008 From: bnrj.rudra at yahoo.com (Rudra Banerjee) Date: Thu, 15 May 2008 18:20:58 +0530 (IST) Subject: [Pw_forum] print time Message-ID: <162045.80978.qm@web94102.mail.in2.yahoo.com> i am sorry...its "print_clock_pw.f90"...actually i tried...but given that it depends on so many module, specially mo_global, i failed to make it run for my own code -- Rudra JRF; SNBNCBS http://www.bose.res.in/~rudra A bus station is where a bus stops. A train station is where a train stops. On my desk I have a work station. Please, if possible, don't send me MS Word or PowerPoint attachments Why?See: http://www.gnu..org/philosophy/no-word-attachments.html ----- Original Message ---- From: Paolo Giannozzi To: PWSCF Forum Sent: Thursday, 15 May, 2008 5:41:28 PM Subject: Re: [Pw_forum] print time Rudra Banerjee wrote: > Dear developers, > can you plz provide me a stand alone version of print_time_pw ? there is no such thing as "print_time_pw": $ grep -i print_time_pw */*f90 $ Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From Chandigarh to Chennai - find friends all over India. Go to http://in.promos.yahoo.com/groups/citygroups/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080515/0bfb27c9/attachment.htm From giannozz at nest.sns.it Thu May 15 15:04:24 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 15 May 2008 15:04:24 +0200 Subject: [Pw_forum] print time In-Reply-To: <162045.80978.qm@web94102.mail.in2.yahoo.com> References: <162045.80978.qm@web94102.mail.in2.yahoo.com> Message-ID: <482C34D8.80307@nest.sns.it> Rudra Banerjee wrote: > i am sorry...its "print_clock_pw.f90"...actually i tried...but given > that it depends on so many module, specially mo_global, i failed to make > it run for my own code what you need is "Modules/clocks.f90", that depends on very few variables from very few external modules, all of which can be trivially eliminated or replaced Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From bnrj.rudra at yahoo.com Thu May 15 15:27:02 2008 From: bnrj.rudra at yahoo.com (Rudra Banerjee) Date: Thu, 15 May 2008 18:57:02 +0530 (IST) Subject: [Pw_forum] print time Message-ID: <906333.2145.qm@web94102.mail.in2.yahoo.com> right, but external file "scnds" is what sausing the trouble -- Rudra JRF; SNBNCBS http://www.bose.res.in/~rudra A bus station is where a bus stops. A train station is where a train stops. On my desk I have a work station. Please, if possible, don't send me MS Word or PowerPoint attachments Why?See: http://www.gnu.org/philosophy/no-word-attachments.html ----- Original Message ---- From: Paolo Giannozzi To: PWSCF Forum Sent: Thursday, 15 May, 2008 6:34:24 PM Subject: Re: [Pw_forum] print time Rudra Banerjee wrote: > i am sorry...its "print_clock_pw.f90"...actually i tried...but given > that it depends on so many module, specially mo_global, i failed to make > it run for my own code what you need is "Modules/clocks.f90", that depends on very few variables from very few external modules, all of which can be trivially eliminated or replaced Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum Explore your hobbies and interests. Go to http://in.promos.yahoo.com/groups/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080515/0cc7160c/attachment.htm From giannozz at nest.sns.it Thu May 15 15:54:23 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 15 May 2008 15:54:23 +0200 Subject: [Pw_forum] print time In-Reply-To: <906333.2145.qm@web94102.mail.in2.yahoo.com> References: <906333.2145.qm@web94102.mail.in2.yahoo.com> Message-ID: <482C408F.3040505@nest.sns.it> Rudra Banerjee wrote: > right, but external file "scnds" is what sausing the trouble it is not an external file but an external routine. scnds() returns a real (double poreciosion) variable containing elapsed time in seconds. In Q-E scnds() is a C routine, because it is hard to find a portable fortran routine performing such a task: clib/cptimer.c Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From eariel99 at gmail.com Thu May 15 19:36:37 2008 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Thu, 15 May 2008 13:36:37 -0400 Subject: [Pw_forum] acml - mkl Message-ID: Dear Sagar, I am not sure if configure detects the acml library. Recently it did not work for me. In case that configure does not detect the ACML, after you run ./configure, edit the file make.sys and modify the last line, to appear like this LIBS = /opt/acml4.1.0/ifort64/lib/libacml.a $(MPI_LIBS) $(MASS_LIBS) $(PGPLOT_LIBS) $(LD_LIBS) Note that /opt/acml4.1.0 is the directory where I placed the ACML in my PC. Use the appropriate directory in your system. I also have one PC with processor AMD 64 X2, the operating system has a strange architecture x86_64 (as given by the command uname -a), but the intel compiler that works is 32bits , the emt64 version does not work for me in this machine. In this machine, I compiled using LIBS = /opt/acml4.1.0/ifort32/lib/libacml.a $(MPI_LIBS) $(MASS_LIBS) $(PGPLOT_LIBS) $(LD_LIBS) Regards Eduardo ---------- Mensaje reenviado ---------- > From: ambavale sagar > To: pwforum que-ans > Date: Tue, 13 May 2008 12:01:16 +0530 (IST) > Subject: [Pw_forum] acml - mkl > Dear Pwscf users, > I have x86_64 (i.e. AMD64) architacture machine with Xeon (x5450-quad core) > processors having dual cpu. I have installed intel fortran compiler, c > compiler and mkl. But as i compile espresso4cvs2 version it does not > recognise BLAS,LAPACK libraries. Must i install ACML as i have AMD > architacture? During compilation of acml i couldn't find driver.f( They say > that driver.f is application program). What should be the procedure? > One more question: Is it possible to have Xeon processors with ia-64 > architacture? > > regards > Sagar Ambavale > Research Student > The M.S.University of Baroda > India > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080515/da40ea56/attachment.htm From giannozz at nest.sns.it Thu May 15 21:04:00 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 15 May 2008 21:04:00 +0200 Subject: [Pw_forum] acml - mkl In-Reply-To: References: Message-ID: <45ED6083-AC04-4F5A-B0B6-882E5FBA73C4@nest.sns.it> On May 15, 2008, at 19:36 , Eduardo Ariel Menendez Proupin wrote: > I am not sure if configure detects the acml library. not when the chosen compiler is ifort Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From asafis at yahoo.com.br Thu May 15 21:04:52 2008 From: asafis at yahoo.com.br (=?iso-8859-1?q?=C1lvaro=20Alves?=) Date: Thu, 15 May 2008 16:04:52 -0300 (ART) Subject: [Pw_forum] Starting magnetization Message-ID: <191161.50932.qm@web52304.mail.re2.yahoo.com> Hello everyone. Is there a limit to the definition of different atomic species for the same type atomic. For example, N1 N2, N2, N4. I need this procedure for several atomic type (N, O, C). Sincerely, Alvaro Abra sua conta no Yahoo! Mail, o ?nico sem limite de espa?o para armazenamento! http://br.mail.yahoo.com/ From akohlmey at cmm.chem.upenn.edu Thu May 15 20:53:11 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Thu, 15 May 2008 14:53:11 -0400 (EDT) Subject: [Pw_forum] Starting magnetization In-Reply-To: <191161.50932.qm@web52304.mail.re2.yahoo.com> References: <191161.50932.qm@web52304.mail.re2.yahoo.com> Message-ID: On Thu, 15 May 2008, ?lvaro Alves wrote: AA> Hello everyone. Is there a limit to the definition of hello alvaro, AA> different atomic species for the same type atomic. For AA> example, N1 N2, N2, N4. I need this procedure for AA> several atomic type (N, O, C). yes. the parameter ntypx determins the maximum number of atom type entries. it is set in Modules/parameters.f90 and the default value is 10. cheers, axel. AA> AA> Sincerely, Alvaro AA> AA> AA> Abra sua conta no Yahoo! Mail, o ?nico sem limite de espa?o para armazenamento! AA> http://br.mail.yahoo.com/ AA> _______________________________________________ AA> Pw_forum mailing list AA> Pw_forum at pwscf.org AA> http://www.democritos.it/mailman/listinfo/pw_forum AA> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From asafis at yahoo.com.br Thu May 15 22:03:40 2008 From: asafis at yahoo.com.br (=?iso-8859-1?q?=C1lvaro=20Alves?=) Date: Thu, 15 May 2008 17:03:40 -0300 (ART) Subject: [Pw_forum] Starting magnetization In-Reply-To: Message-ID: <531775.96213.qm@web52304.mail.re2.yahoo.com> Hi Axel, thank you for information. Can I change this value and recompile the program? Sincerely, Alvaro --- Axel Kohlmeyer escreveu: > On Thu, 15 May 2008, ?lvaro Alves wrote: > > AA> Hello everyone. Is there a limit to the > definition of > > hello alvaro, > > AA> different atomic species for the same type > atomic. For > AA> example, N1 N2, N2, N4. I need this procedure > for > AA> several atomic type (N, O, C). > > yes. the parameter ntypx determins the maximum > number > of atom type entries. it is set in > Modules/parameters.f90 > and the default value is 10. > > cheers, > axel. > > > AA> > AA> Sincerely, Alvaro > AA> > AA> > AA> Abra sua conta no Yahoo! Mail, o ?nico sem > limite de espa?o para armazenamento! > AA> http://br.mail.yahoo.com/ > AA> _______________________________________________ > AA> Pw_forum mailing list > AA> Pw_forum at pwscf.org > AA> > http://www.democritos.it/mailman/listinfo/pw_forum > AA> > > -- > ======================================================================= > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu > http://www.cmm.upenn.edu > Center for Molecular Modeling -- University > of Pennsylvania > Department of Chemistry, 231 S.34th Street, > Philadelphia, PA 19104-6323 > tel: 1-215-898-1582, fax: 1-215-573-6233, > office-tel: 1-215-898-5425 > ======================================================================= > If you make something idiot-proof, the universe > creates a better idiot.> _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > Abra sua conta no Yahoo! Mail, o ?nico sem limite de espa?o para armazenamento! http://br.mail.yahoo.com/ From akohlmey at cmm.chem.upenn.edu Thu May 15 21:39:22 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Thu, 15 May 2008 15:39:22 -0400 (EDT) Subject: [Pw_forum] Starting magnetization In-Reply-To: <531775.96213.qm@web52304.mail.re2.yahoo.com> References: <531775.96213.qm@web52304.mail.re2.yahoo.com> Message-ID: On Thu, 15 May 2008, ?lvaro Alves wrote: AA> Hi Axel, thank you for information. Can I change this AA> value and recompile the program? if you change the tiniest bit of the Q-E source code, your computer will immediately initiate its secret self-destruct procedure upon the first execution of an executable compiled from thusly modified sources. if you don't mind that, just go ahead and be prepared for the worst. ;-) axel. AA> AA> Sincerely, Alvaro -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From zx3 at rice.edu Fri May 16 02:05:49 2008 From: zx3 at rice.edu (zx3 at rice.edu) Date: Thu, 15 May 2008 19:05:49 -0500 Subject: [Pw_forum] bug report in PWCOND Message-ID: <1210896349.482ccfddbe238@webmail.mail.rice.edu> Dear all: In CVS_080208 and previous version, File: PWCOND/local.f90 Line 410: ------------------------------------------------------------- INTEGER :: nrx, nry, fftxy(-nrx:nrx, -nrx:nry), & number, n1, n2 ------------------------------------------------------------- should be ------------------------------------------------------------- INTEGER :: nrx, nry, fftxy(-nrx:nrx, -nry:nry), & number, n1, n2 ------------------------------------------------------------- where -nry was mistyped as -nrx Best, Zhiping From coldwind1978 at yahoo.com.cn Fri May 16 04:01:14 2008 From: coldwind1978 at yahoo.com.cn (=?gb2312?q?=D5=EB=D2=B6=20=D6=EC?=) Date: Fri, 16 May 2008 10:01:14 +0800 (CST) Subject: [Pw_forum] what's the meaning of error in compiler of sun solaris? Message-ID: <685489.25360.qm@web15803.mail.cnb.yahoo.com> Dear users: I want to compile pwscf in sun solaris 9.0. when i make pw, the error appears as following: ld: fatal: Symbol referencing errors. No output written to pw.x *** Error code 1 make: Fatal error: Command failed for target `pw.x' Current working directory /zzy/espresso-4.0/PW *** Error code 1 make: Fatal error: Command failed for target `pw' what is the meaning of the error, and how to deal with it? Please give me some suggestios. Regards zhuzhenye --------------------------------- ???????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080516/d8a30c2d/attachment.htm From sagarambavale at yahoo.co.in Fri May 16 07:45:23 2008 From: sagarambavale at yahoo.co.in (ambavale sagar) Date: Fri, 16 May 2008 11:15:23 +0530 (IST) Subject: [Pw_forum] acml-mkl Message-ID: <511744.94911.qm@web94608.mail.in2.yahoo.com> AS> I have x86_64 (i.e. AMD64) architacture machine with Xeon AS> (x5450-quad core) processors having dual cpu. I have installed intel AS> fortran compiler, c compiler and mkl. But as i compile espresso4cvs2 AS> version it does not recognise BLAS,LAPACK libraries. AK>if configure does not find MKL, it either means you have not AK>installed it correctly or to a location that configure does not AK>know about. check the config.log file and simply adapt the make.sys AK>file manually according to the MKL user's guide (RTFM!!). hi, My config.log file shows that it detect the mkl library at a standard place but finds it incompatible. The part of config.log file looks like : ................. .............. configure:5894: checking for library containing dgemm configure:5907: ifort -o conftest -O2 -assume byterecl -nomodule -i-static -openmp -L/opt/intel/mkl/10.0.1.014/lib/em64t conftest.f >&5 ld: skipping incompatible /opt/intel/mkl/10.0.1.014/lib/em64t/libguide.a when searching for -lguide /tmp/ifortMq0fkI.o: In function `MAIN__': conftest.f:(.text+0x2b): undefined reference to `dgemm_' configure:5913: $? = 1 configure: failed program was: | program main | call dgemm | end configure:5945: ifort -o conftest -O2 -assume byterecl -nomodule -i-static -openmp -L/opt/intel/mkl/10.0.1.014/lib/em64t conftest.f -lmkl_em64t >&5 ld: skipping incompatible /opt/intel/mkl/10.0.1.014/lib/em64t/libmkl_intel_lp64..a when searching for libmkl_intel_lp64.a ld: cannot find libmkl_intel_lp64.a configure:5951: $? = 1 configure: failed program was: | program main | call dgemm | end configure:5979: result: no configure:5894: checking for library containing dgemm configure:5907: ifort -o conftest -O2 -assume byterecl -nomodule -i-static -openmp -L/opt/intel/mkl*/lib/em64t conftest.f >&5 ..................... ...................... What is your Emotional Quotient? Find out here - http://in.search.yahoo.com/search?&fr=na_onnetwork_mail_taglines&ei=UTF-8&rd=r1&p=emotional+quotient -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080516/e361dee8/attachment.htm From vparkash at mtu.edu Fri May 16 08:43:01 2008 From: vparkash at mtu.edu (Vidur Parkash) Date: Thu, 15 May 2008 23:43:01 -0700 (PDT) Subject: [Pw_forum] DOS Units Message-ID: <290135.76297.qm@web35406.mail.mud.yahoo.com> A simple question In what units does dos.x return the values of density of states? Is it states / eV / m^3 or something else? Vidur Vidur Parkash Electrical & Computer Engineering Michigan Technological University 716 EERC, 1400 Townsend Drive Houghton, MI-49931, USA Tel: 1-906-487-0023 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080515/1dfaa65e/attachment.htm From lanhaiping at gmail.com Fri May 16 08:56:15 2008 From: lanhaiping at gmail.com (lan haiping) Date: Fri, 16 May 2008 14:56:15 +0800 Subject: [Pw_forum] DOS Units In-Reply-To: <290135.76297.qm@web35406.mail.mud.yahoo.com> References: <290135.76297.qm@web35406.mail.mud.yahoo.com> Message-ID: from dos.f90: ! Output: ! ! The total DOS (states/eV plotted vs E in eV) is written to file "fildos" regards, Hai-Ping On Fri, May 16, 2008 at 2:43 PM, Vidur Parkash wrote: > A simple question > > In what units does dos.x return the values of density of states? Is it > states / eV / m^3 or something else? > > Vidur > > > Vidur Parkash > Electrical & Computer Engineering > Michigan Technological University > 716 EERC, 1400 Townsend Drive > Houghton, MI-49931, USA > Tel: 1-906-487-0023 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080516/a7344318/attachment.htm From djaithania at hotmail.com Fri May 16 08:51:12 2008 From: djaithania at hotmail.com (hania djani-ait aissa) Date: Fri, 16 May 2008 06:51:12 +0000 Subject: [Pw_forum] polarization calculation in ferroelectrics Message-ID: Dear all, I am new PWSCF user, I am trying to calculate polarization in Bi4Ti3O12. this material is centered tetragonal in its paraelectric phase and orthorhombic bases centered in its ferroelectric one. having in mind the papers of Resta, King-smith and Vanderbilt, i have to fix the initial state with P=0 and then make a small displacement of a subgroup with respect to others. my question is: what will be the initial structure to put as input? the paraelectric tetragonal one with its symmetry center, or the ferroelectric one were i force the orthorhombic structure to be centered , relaxing all atoms and making the small displacement?? thank you in advance, Hania H. Djani Ait Aissa Center of Development of Advanced Technologies Haouch Oukil, PoBox.017, Algiers, Algeria _________________________________________________________________ Appelez vos amis de PC ? PC -- C'EST GRATUIT http://get.live.com/messenger/overview From dalcorso at sissa.it Fri May 16 09:08:33 2008 From: dalcorso at sissa.it (Dal Corso Andrea) Date: Fri, 16 May 2008 09:08:33 +0200 Subject: [Pw_forum] bug report in PWCOND In-Reply-To: <1210896349.482ccfddbe238@webmail.mail.rice.edu> References: <1210896349.482ccfddbe238@webmail.mail.rice.edu> Message-ID: <1210921713.3353.2.camel@dhpc-5-03.sissa.it> Dear Zhiping, You are right, thank you. I will correct the cvs version. Andrea Dal Corso On Thu, 2008-05-15 at 19:05 -0500, zx3 at rice.edu wrote: > Dear all: > In CVS_080208 and previous version, File: PWCOND/local.f90 > Line 410: > ------------------------------------------------------------- > INTEGER :: nrx, nry, fftxy(-nrx:nrx, -nrx:nry), & > number, n1, n2 > ------------------------------------------------------------- > should be > ------------------------------------------------------------- > INTEGER :: nrx, nry, fftxy(-nrx:nrx, -nry:nry), & > number, n1, n2 > ------------------------------------------------------------- > where -nry was mistyped as -nrx > Best, > Zhiping > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Andrea Dal Corso Tel. 0039-040-3787428 SISSA, Via Beirut 2/4 Fax. 0039-040-3787528 34014 Trieste (Italy) e-mail: dalcorso at sissa.it From paulatto at sissa.it Fri May 16 09:34:45 2008 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 16 May 2008 09:34:45 +0200 (CEST) Subject: [Pw_forum] acml - mkl In-Reply-To: References: Message-ID: <14099.79.1.239.82.1210923285.squirrel@webmail.sissa.it> On Thu, May 15, 2008 19:36, Eduardo Ariel Menendez Proupin wrote: > the operating system has a strange architecture x86_64 (as given by the > command uname -a), but the As far as I know, x86_64 is the standard name for 64bit architectures AMD64 and Intel64 (not itanium). -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) +39 040 3787 511 http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From paulatto at sissa.it Fri May 16 09:40:39 2008 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 16 May 2008 09:40:39 +0200 (CEST) Subject: [Pw_forum] Starting magnetization In-Reply-To: References: <191161.50932.qm@web52304.mail.re2.yahoo.com> Message-ID: <14173.79.1.239.82.1210923639.squirrel@webmail.sissa.it> On Thu, May 15, 2008 20:53, Axel Kohlmeyer wrote: > yes. the parameter ntypx determins the maximum number > of atom type entries. it is set in Modules/parameters.f90 > and the default value is 10. In version 4.0 there only a few (maybe zero), static arrays of size ntyp. I think we could have removed that limit for the next release, but there is not enough time now. It will be done for 4.1 bye -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) +39 040 3787 511 http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From paulatto at sissa.it Fri May 16 09:44:21 2008 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 16 May 2008 09:44:21 +0200 (CEST) Subject: [Pw_forum] what's the meaning of error in compiler of sun solaris? In-Reply-To: <685489.25360.qm@web15803.mail.cnb.yahoo.com> References: <685489.25360.qm@web15803.mail.cnb.yahoo.com> Message-ID: <14222.79.1.239.82.1210923861.squirrel@webmail.sissa.it> On Fri, May 16, 2008 04:01, ???? ?? wrote: > what is the meaning of the error, and how to deal with it? Please give > me some suggestios. Dear Zhuzhenye, you could have provided a few more lines to help us figure out what is going on. From what I can see, it looks like you are missing some basic development libraries. I'm no Solaris guru, but I can imagine there are some development packages you can install in the system. Have you checked they are actually installed? regards P.S. please provide your affiliation when writing to this mailing list -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) +39 040 3787 511 http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From coldwind1978 at yahoo.com.cn Fri May 16 12:54:46 2008 From: coldwind1978 at yahoo.com.cn (=?gb2312?q?=D5=EB=D2=B6=20=D6=EC?=) Date: Fri, 16 May 2008 18:54:46 +0800 (CST) Subject: [Pw_forum] =?gb2312?b?16q3oqO6IHdoYXQncyB0aGUgbWVhbmluZyBvZiBl?= =?gb2312?b?cnJvciBpbiBjb21waWxlciBvZiBzdW4gc29sYXJpcz8=?= Message-ID: <423629.23615.qm@web15807.mail.cnb.yahoo.com> ?????????? --------------------------------- ???????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080516/2cb55a5b/attachment.htm -------------- next part -------------- An embedded message was scrubbed... From: =?gb2312?q?=D5=EB=D2=B6=20=D6=EC?= Subject: what's the meaning of error in compiler of sun solaris? Date: Fri, 16 May 2008 10:01:14 +0800 (CST) Size: 2763 Url: http://www.democritos.it/pipermail/pw_forum/attachments/20080516/2cb55a5b/attachment.eml From lanhaiping at gmail.com Fri May 16 13:25:46 2008 From: lanhaiping at gmail.com (lan haiping) Date: Fri, 16 May 2008 19:25:46 +0800 Subject: [Pw_forum] =?gb2312?b?16q3oqO6IHdoYXQncyB0aGUgbWVhbmluZyBvZiBl?= =?gb2312?b?cnJvciBpbiBjb21waWxlciBvZiBzdW4gc29sYXJpcz8=?= In-Reply-To: <423629.23615.qm@web15807.mail.cnb.yahoo.com> References: <423629.23615.qm@web15807.mail.cnb.yahoo.com> Message-ID: Why do you repeat your email's content ? This is a mail-list, and every thread will be kept. Just forwarding your previous mail to this mai-list won't help your problem solve . You should give more detailed compilation environments 2008/5/16 ?? ? : > > > ?????????? > > ------------------------------ > ???????????? > > ---------- Forwarded message ---------- > From: ?? ? > To: pw_forum at pwscf.org > Date: Fri, 16 May 2008 10:01:14 +0800 (CST) > Subject: what's the meaning of error in compiler of sun solaris? > Dear users: > I want to compile pwscf in sun solaris 9.0. when i make pw, the error > appears as following: > ld: fatal: Symbol referencing errors. No output written to > pw.x > *** Error code 1 > make: Fatal error: Command failed for target `pw.x' > Current working directory /zzy/espresso-4.0/PW > *** Error code 1 > make: Fatal error: Command failed for target `pw' > what is the meaning of the error, and how to deal with it? Please give me > some suggestios. > > Regards > > zhuzhenye > > > ------------------------------ > ???????????? > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080516/9b646261/attachment-0001.htm From giannozz at nest.sns.it Fri May 16 13:57:34 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 16 May 2008 13:57:34 +0200 Subject: [Pw_forum] what's the meaning of error in compiler of sun solaris? In-Reply-To: <685489.25360.qm@web15803.mail.cnb.yahoo.com> References: <685489.25360.qm@web15803.mail.cnb.yahoo.com> Message-ID: <482D76AE.3030607@nest.sns.it> ?? ? wrote: > I want to compile pwscf in sun solaris 9.0. when i make pw, the > error appears as following: > ld: fatal: Symbol referencing errors. No output written to pw.x >[...] what is the meaning of the error, and how to deal with it? Please >give me some suggestions. In my short experience with solaris 10, I managed to compile PWscf, and the difficult part was to understand which fortran and C compiler and linker to use. The machine I got had Sun fortran compiler (but it was well hidden) and a number of C compilers (do not remember which was the good one). So my suggestion is to understand what is in your machine and to try to compile a simple job first. In the new version, "configure" should recognize PC with Solaris, if properly set up (i.e. with a working combination of fortran and C and linker in your path) Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From quevedin at gmail.com Fri May 16 17:16:17 2008 From: quevedin at gmail.com (Lucas Fernandez Seivane) Date: Fri, 16 May 2008 17:16:17 +0200 Subject: [Pw_forum] problem with neb calculation In-Reply-To: <43468F03.000005.25318@soapbox.yandex.ru> References: <20051007144345.62427.qmail@web60312.mail.yahoo.com> <43468F03.000005.25318@soapbox.yandex.ru> Message-ID: <2ebe300a0805160816o2627769fqa152b6eb96e2dd5b@mail.gmail.com> Dear Sir I am trying to compile espresso 4.0 but I always fall with this problem. Do you have a make.sys for ppc970 + Linux? Regards Lucas Fern?ndez Seivane On Fri, Oct 7, 2005 at 5:06 PM, Sergey Lisenkov wrote: >>Hi, >> >>Yes, so strange. Does it depend on bmaxdata size? > > For me it seems to be very strange. On our IBM PPC970 cluster (OS Linux) we cannot use -qbmaxdata option, but I reproduce a problem reported by Vivek. > > Sergey > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From paulatto at sissa.it Fri May 16 17:34:55 2008 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 16 May 2008 17:34:55 +0200 (CEST) Subject: [Pw_forum] problem with neb calculation In-Reply-To: <2ebe300a0805160816o2627769fqa152b6eb96e2dd5b@mail.gmail.com> References: <20051007144345.62427.qmail@web60312.mail.yahoo.com> <43468F03.000005.25318@soapbox.yandex.ru> <2ebe300a0805160816o2627769fqa152b6eb96e2dd5b@mail.gmail.com> Message-ID: <25053.147.122.5.216.1210952095.squirrel@webmail.sissa.it> On Fri, May 16, 2008 17:16, Lucas Fernandez Seivane wrote: > I am trying to compile espresso 4.0 but I always fall with this > problem. Do you have a make.sys for ppc970 + Linux? Dear Lucas, which problem? regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) +39 040 3787 511 http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From quevedin at gmail.com Fri May 16 17:50:30 2008 From: quevedin at gmail.com (Lucas Fernandez Seivane) Date: Fri, 16 May 2008 17:50:30 +0200 Subject: [Pw_forum] problem with neb calculation In-Reply-To: <25053.147.122.5.216.1210952095.squirrel@webmail.sissa.it> References: <20051007144345.62427.qmail@web60312.mail.yahoo.com> <43468F03.000005.25318@soapbox.yandex.ru> <2ebe300a0805160816o2627769fqa152b6eb96e2dd5b@mail.gmail.com> <25053.147.122.5.216.1210952095.squirrel@webmail.sissa.it> Message-ID: <2ebe300a0805160850n38597684icabd3b61240f5ed@mail.gmail.com> Hi to the FORUM Sorry about the former message, I didn't put it in context. I am compiling espresso 4.0 on a ppc64 linux cluster, and I have a well known problem about ZHPEV. I am able to generate a nice pw.x, that works fine for many things but not for the example25. Also, I had a 3.2.2 binary that was able to run LDA+U calculations, but it also fails with this example, as enter write_ns U( 1) = 0.0000 U( 2) = 0.0000 U( 3) = 0.0000 alpha( 1) = 0.0000 alpha( 2) = 0.0000 alpha( 3) = 0.0000 atom 3 Tr[ns(na)]= 6.0000000 ** On entry to ZHPEV parameter number 1 had an illegal value Any help would be greatly apreciated. On Fri, May 16, 2008 at 5:34 PM, Lorenzo Paulatto wrote: > > On Fri, May 16, 2008 17:16, Lucas Fernandez Seivane wrote: >> I am trying to compile espresso 4.0 but I always fall with this >> problem. Do you have a make.sys for ppc970 + Linux? > > Dear Lucas, > which problem? > > regards > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > +39 040 3787 511 > http://people.sissa.it/~paulatto/ > > > ---------------------------------------------------------------- > SISSA Webmail https://webmail.sissa.it/ > Powered by SquirrelMail http://www.squirrelmail.org/ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From akohlmey at cmm.chem.upenn.edu Fri May 16 17:35:38 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Fri, 16 May 2008 11:35:38 -0400 (EDT) Subject: [Pw_forum] acml-mkl In-Reply-To: <511744.94911.qm@web94608.mail.in2.yahoo.com> References: <511744.94911.qm@web94608.mail.in2.yahoo.com> Message-ID: On Fri, 16 May 2008, ambavale sagar wrote: AS> My config.log file shows that it detect the mkl library at a AS> standard place but finds it incompatible. The part of config.log file looks like : AS> ................. AS> .............. AS> configure:5894: checking for library containing dgemm AS> configure:5907: ifort -o conftest -O2 -assume byterecl -nomodule AS> -i-static -openmp -L/opt/intel/mkl/10.0.1.014/lib/em64t conftest.f >&5 AS> ld: skipping incompatible AS> /opt/intel/mkl/10.0.1.014/lib/em64t/libguide.a when searching for AS> -lguide AS> /tmp/ifortMq0fkI.o: In function `MAIN__': AS> conftest.f:(.text+0x2b): undefined reference to `dgemm_' that looks like your fortran compiler is producing 32-bit code and not 64-bit code. most likely your installation is messed up. it is hard enough to write automatic detection for compilers and libraries that works on reasonably installed machines, you cannot expect that to work on inconsistent installations. you'll have to write the corresponding sections of make.sys (it is not _that_ hard, just read the comments) by hand or clean up your installation. axel. -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From akohlmey at cmm.chem.upenn.edu Fri May 16 17:38:19 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Fri, 16 May 2008 11:38:19 -0400 (EDT) Subject: [Pw_forum] acml - mkl In-Reply-To: <14099.79.1.239.82.1210923285.squirrel@webmail.sissa.it> References: <14099.79.1.239.82.1210923285.squirrel@webmail.sissa.it> Message-ID: On Fri, 16 May 2008, Lorenzo Paulatto wrote: LP> LP> On Thu, May 15, 2008 19:36, Eduardo Ariel Menendez Proupin wrote: LP> > the operating system has a strange architecture x86_64 (as given by the LP> > command uname -a), but the LP> LP> As far as I know, x86_64 is the standard name for 64bit architectures LP> AMD64 and Intel64 (not itanium). there is no standard name for this. x86_64 is what the linux folks choose to represent it. AMD refers/referred to it as AMD64 and Intel as EM64t. cheers, axel. LP> LP> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From akohlmey at cmm.chem.upenn.edu Fri May 16 17:43:12 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Fri, 16 May 2008 11:43:12 -0400 (EDT) Subject: [Pw_forum] problem with neb calculation In-Reply-To: <2ebe300a0805160850n38597684icabd3b61240f5ed@mail.gmail.com> References: <20051007144345.62427.qmail@web60312.mail.yahoo.com> <43468F03.000005.25318@soapbox.yandex.ru> <2ebe300a0805160816o2627769fqa152b6eb96e2dd5b@mail.gmail.com> <25053.147.122.5.216.1210952095.squirrel@webmail.sissa.it> <2ebe300a0805160850n38597684icabd3b61240f5ed@mail.gmail.com> Message-ID: On Fri, 16 May 2008, Lucas Fernandez Seivane wrote: LFS> Hi to the FORUM LFS> LFS> Sorry about the former message, I didn't put it in context. I am LFS> compiling espresso 4.0 on a ppc64 linux cluster, and I have a well LFS> known problem about ZHPEV. I am able to generate a nice pw.x, that LFS> works fine for many things but not for the example25. Also, I had a LFS> 3.2.2 binary that was able to run LDA+U calculations, but it also LFS> fails with this example, as LFS> enter write_ns LFS> U( 1) = 0.0000 U( 2) = 0.0000 U( 3) = 0.0000 LFS> alpha( 1) = 0.0000 alpha( 2) = 0.0000 alpha( 3) = 0.0000 LFS> atom 3 Tr[ns(na)]= 6.0000000 LFS> ** On entry to ZHPEV parameter number 1 had an illegal value LFS> LFS> Any help would be greatly apreciated. so what is _your_ make.sys? are you using ESSL? there used to be a number of "LAPACK" calls in ESSL that use a different calling sequence (for historical reasons). have you tried compiling ZHPEV from original LAPACK source and link with it first? cheers, axel. LFS> On Fri, May 16, 2008 at 5:34 PM, Lorenzo Paulatto wrote: LFS> > LFS> > On Fri, May 16, 2008 17:16, Lucas Fernandez Seivane wrote: LFS> >> I am trying to compile espresso 4.0 but I always fall with this LFS> >> problem. Do you have a make.sys for ppc970 + Linux? LFS> > LFS> > Dear Lucas, LFS> > which problem? LFS> > LFS> > regards LFS> > LFS> > -- LFS> > Lorenzo Paulatto LFS> > SISSA & DEMOCRITOS (Trieste) LFS> > +39 040 3787 511 LFS> > http://people.sissa.it/~paulatto/ LFS> > LFS> > LFS> > ---------------------------------------------------------------- LFS> > SISSA Webmail https://webmail.sissa.it/ LFS> > Powered by SquirrelMail http://www.squirrelmail.org/ LFS> > LFS> > _______________________________________________ LFS> > Pw_forum mailing list LFS> > Pw_forum at pwscf.org LFS> > http://www.democritos.it/mailman/listinfo/pw_forum LFS> > LFS> _______________________________________________ LFS> Pw_forum mailing list LFS> Pw_forum at pwscf.org LFS> http://www.democritos.it/mailman/listinfo/pw_forum LFS> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From eariel99 at gmail.com Fri May 16 18:46:25 2008 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Fri, 16 May 2008 12:46:25 -0400 Subject: [Pw_forum] acml-mkl Message-ID: Dear Sagar, Please, run the following commands and let me know the output uname -a ifort -V ./configure (in the ESPRESSO directory) Eduardo > ---------- Mensaje reenviado ---------- > From: ambavale sagar > To: pwforum que-ans > Date: Fri, 16 May 2008 11:15:23 +0530 (IST) > Subject: Re: [Pw_forum] acml-mkl > AS> I have x86_64 (i.e. AMD64) architacture machine with Xeon > AS> (x5450-quad core) processors having dual cpu. I have installed intel > AS> fortran compiler, c compiler and mkl. But as i compile espresso4cvs2 > AS> version it does not recognise BLAS,LAPACK libraries. > > AK>if configure does not find MKL, it either means you have not > AK>installed it correctly or to a location that configure does not > AK>know about. check the config.log file and simply adapt the make.sys > AK>file manually according to the MKL user's guide (RTFM!!). > > hi, > My config.log file shows that it detect the mkl library at a standard place > but finds it incompatible. The part of config.log file looks like : > ................. > .............. > configure:5894: checking for library containing dgemm > configure:5907: ifort -o conftest -O2 -assume byterecl -nomodule -i-static > -openmp -L/opt/intel/mkl/10.0.1.014/lib/em64t conftest.f >&5 > ld: skipping incompatible /opt/intel/mkl/10.0.1.014/lib/em64t/libguide.awhen searching for -lguide > /tmp/ifortMq0fkI.o: In function `MAIN__': > conftest.f:(.text+0x2b): undefined reference to `dgemm_' > configure:5913: $? = 1 > configure: failed program was: > | program main > | call dgemm > | end > configure:5945: ifort -o conftest -O2 -assume byterecl -nomodule -i-static > -openmp -L/opt/intel/mkl/10.0.1.014/lib/em64t conftest.f -lmkl_em64t > >&5 > ld: skipping incompatible /opt/intel/mkl/ > 10.0.1.014/lib/em64t/libmkl_intel_lp64..a when searching for > libmkl_intel_lp64.a > ld: cannot find libmkl_intel_lp64.a > configure:5951: $? = 1 > configure: failed program was: > | program main > | call dgemm > | end > configure:5979: result: no > configure:5894: checking for library containing dgemm > configure:5907: ifort -o conftest -O2 -assume byterecl -nomodule -i-static > -openmp -L/opt/intel/mkl*/lib/em64t conftest.f >&5 > > ... > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080516/e5eadd09/attachment.htm From chen_shao_hua197 at yahoo.com.tw Fri May 16 21:44:07 2008 From: chen_shao_hua197 at yahoo.com.tw (=?big5?q?=B3=AF=20=A4=D6=B5=D8?=) Date: Sat, 17 May 2008 03:44:07 +0800 (CST) Subject: [Pw_forum] About nelec and tot_charge again In-Reply-To: <200712261827.44933.giannozz@nest.sns.it> Message-ID: <882635.16279.qm@web73013.mail.tp2.yahoo.com> Dear Paolo and other forum's members, I heard there is a method call "Rigid Band Approximation"(RBA). In order to shift Fermi level to conduction band or valence band in semiconductor, does it make sense just set "nelec" parameter only ? max PhD candidate Physics department, National Taiwan University, Taiwan. --- Paolo Giannozzi ?? > On Monday 24 December 2007 12:11, oulihui666 wrote: > > > I intend to ask wheather I could add a extra > electron and +1 charge > > simultaneously? > > you can add an extra electron by setting variable > "nelec" to the desired > charges. The code will automatically add a > neutralizing background (it > must! the energy of a charged supercell is > infinite). In practice, the energy > is calculated as usual, but the divergent terms will > be calculated as if > the system was neutral. For a molecule the energy so > obtained will > converge for increasing size of the supercell to the > true energy of the > charged molecule; there are various tricks to > speedup the convergence > (e.g. the Makov-Payne correction). Formation > energies of charged defects > can also be calculated but it is a more tricky > business. > > By the way, all this has been explained 2n+1 times. > > Paolo > -- > Paolo Giannozzi, Democritos and Udine University > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > _____________________________________________________________________________________ ??????Yahoo!??????2.0? http://tw.mg0.mail.yahoo.com/dc/landing From sagarambavale at yahoo.co.in Sat May 17 11:32:01 2008 From: sagarambavale at yahoo.co.in (ambavale sagar) Date: Sat, 17 May 2008 15:02:01 +0530 (IST) Subject: [Pw_forum] acml-mkl Message-ID: <195173.55407.qm@web94602.mail.in2.yahoo.com> >Dear Sagar, Dear Sir, Thank you very much for taking interest. >Please, run the following commands and let me know the output Here are the outputs with respective commands. >uname -a Linux localhost.localdomain 2.6.18-8.el5 #1 SMP Fri Jan 26 14:15:14 EST 2007 x86_64 x86_64 x86_64 GNU/Linux >ifort -V Version 10.1 >./configure (in the ESPRESSO directory) [phy at localhost espresso4.0cvs2]$ ./configure checking build system type... x86_64-unknown-linux-gnu checking architecture... amd64 checking for ifort... ifort checking for Fortran 77 compiler default output file name... a.out checking whether the Fortran 77 compiler works... yes checking whether we are cross compiling... yes checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU Fortran 77 compiler... no checking whether ifort accepts -g... yes checking for mpif90... no checking for ifort... ifort checking whether we are using the GNU Fortran 77 compiler... no checking whether ifort accepts -g... yes checking version of ifort... ifort 10.1 setting F90... ifort setting MPIF90... ifort checking for icc... icc checking whether we are using the GNU C compiler... yes checking whether icc accepts -g... yes checking for icc option to accept ANSI C... none needed setting CC... icc checking how to run the C preprocessor... icc -E checking for egrep... grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for int *... yes checking size of int *... 4 checking malloc.h usability... yes checking malloc.h presence... yes checking for malloc.h... yes checking for struct mallinfo.arena... yes checking for ifort... ifort checking whether we are using the GNU Fortran 77 compiler... no checking whether ifort accepts -g... yes setting F77... ifort setting FFLAGS.... -O2 -assume byterecl setting F90FLAGS... $(FFLAGS) -nomodule setting FFLAGS_NOOPT... -O0 -assume byterecl setting CFLAGS... -O3 setting CPP... cpp setting CPPFLAGS... -P -traditional setting LD... ifort setting LDFLAGS... setting AR... ar setting ARFLAGS... ruv setting ARFLAGS_DYNAMIC...ruv checking whether make sets $(MAKE)... yes checking whether Fortran files must be preprocessed... no checking how to get verbose linking output from ifort... -v checking for Fortran libraries of ifort.... -L/opt/intel/fc/10.1.012/lib -L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/32 -L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/32/.. -L/usr/lib -lifport -lifcore -limf -lm -lipgo -lirc -lgcc_s -lirc_s -ldl checking for dummy main to link with Fortran libraries... none checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore checking for library containing dgemm... no in /opt/intel/mkl/10.0.1.014/lib/em64t: checking for library containing dgemm... no in /opt/intel/mkl*/lib/em64t: checking for library containing dgemm... no in /opt/intel/cc/10.1.015/lib: checking for library containing dgemm... no in /opt/intel/fc/10.1.012/lib: checking for library containing dgemm... no checking for library containing dgemm... no in /usr/local/lib: checking for library containing dgemm... no in /cineca/prod/intel/lib: checking for library containing dgemm... no in /opt/intel/cc/10.1.015/lib: checking for library containing dgemm... no in /opt/intel/fc/10.1.012/lib: checking for library containing dgemm.... no checking for library containing dgemm... no in /usr/local/lib: checking for library containing dgemm... no in /cineca/prod/intel/lib: checking for library containing dgemm... no in /opt/intel/cc/10.1.015/lib: checking for library containing dgemm... no in /opt/intel/fc/10.1.012/lib: checking for library containing dgemm... no checking for library containing zggev... no in /usr/local/lib: checking for library containing zggev... no in /cineca/prod/intel/lib: checking for library containing zggev... no in /opt/intel/cc/10.1.015/lib: checking for library containing zggev... no in /opt/intel/fc/10.1.012/lib: checking for library containing zggev.... no setting BLAS_LIBS... ../flib/blas.a setting LAPACK_LIBS... ../flib/lapack.a checking for library containing fftwnd... no in /usr/local/lib: checking for library containing fftwnd... no in /cineca/prod/intel/lib: checking for library containing fftwnd... no in /opt/intel/cc/10.1.015/lib: checking for library containing fftwnd... no in /opt/intel/fc/10.1.012/lib: checking for library containing fftwnd... no setting FFT_LIBS... checking for library containing fftwnd... (cached) no setting MASS_LIBS... checking for library containing mpi_init... no setting MPI_LIBS... checking for library containing mpi_init... (cached) no setting DFLAGS.... -D__INTEL -D__FFTW -D__USE_INTERNAL_FFTW setting IFLAGS... -I../include setting FDFLAGS... $(DFLAGS) checking for ranlib... ranlib setting RANLIB... ranlib configure: creating ./config.status config.status: creating include/fft_defs.h config.status: creating make.sys config.status: creating configure.msg config.status: creating include/c_defs.h config.status: include/c_defs.h is unchanged -------------------------------------------------------------------- ESPRESSO can take advantage of several optimized numerical libraries (essl, fftw, mkl...). This configure script attempts to find them, but may fail if they have been installed in non-standard locations. If a required library is not found, the local copy will be compiled. The following libraries have been found: BLAS_LIBS=../flib/blas.a LAPACK_LIBS=../flib/lapack.a FFT_LIBS= Please check if this is what you expect. If any libraries are missing, you may specify a list of directories to search and retry, as follows: ./configure LIBDIRS="list of directories, separated by spaces" Parallel environment not detected (is this a parallel machine?). Configured for compilation of serial executables. For more info, read the ESPRESSO User's Guide (Doc/users-guide.tex). -------------------------------------------------------------------- configure: success [phy at localhost espresso4.0cvs2]$ regards Sagar Best Jokes, Best Friends, Best Food and more. Go to http://in.promos.yahoo.com/groups/bestofyahoo/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080517/f9948e3e/attachment.htm From sagarambavale at yahoo.co.in Sat May 17 11:32:04 2008 From: sagarambavale at yahoo.co.in (ambavale sagar) Date: Sat, 17 May 2008 15:02:04 +0530 (IST) Subject: [Pw_forum] acml-mkl Message-ID: <101785.93735.qm@web94605.mail.in2.yahoo.com> Dear Sir, Thank you very much for taking interest. >Please, run the following commands and let me know the output Here are the outputs with respective commands. >uname -a Linux localhost.localdomain 2.6.18-8.el5 #1 SMP Fri Jan 26 14:15:14 EST 2007 x86_64 x86_64 x86_64 GNU/Linux >ifort -V Version 10.1 >./configure (in the ESPRESSO directory) [phy at localhost espresso4.0cvs2]$ ./configure checking build system type... x86_64-unknown-linux-gnu checking architecture... amd64 checking for ifort... ifort checking for Fortran 77 compiler default output file name.... a.out checking whether the Fortran 77 compiler works... yes checking whether we are cross compiling... yes checking for suffix of executables.... checking for suffix of object files... o checking whether we are using the GNU Fortran 77 compiler... no checking whether ifort accepts -g.... yes checking for mpif90... no checking for ifort... ifort checking whether we are using the GNU Fortran 77 compiler... no checking whether ifort accepts -g... yes checking version of ifort... ifort 10.1 setting F90... ifort setting MPIF90... ifort checking for icc... icc checking whether we are using the GNU C compiler... yes checking whether icc accepts -g... yes checking for icc option to accept ANSI C... none needed setting CC... icc checking how to run the C preprocessor... icc -E checking for egrep... grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for int *.... yes checking size of int *... 4 checking malloc.h usability... yes checking malloc.h presence... yes checking for malloc.h... yes checking for struct mallinfo.arena... yes checking for ifort... ifort checking whether we are using the GNU Fortran 77 compiler... no checking whether ifort accepts -g... yes setting F77... ifort setting FFLAGS... -O2 -assume byterecl setting F90FLAGS... $(FFLAGS) -nomodule setting FFLAGS_NOOPT... -O0 -assume byterecl setting CFLAGS... -O3 setting CPP... cpp setting CPPFLAGS... -P -traditional setting LD... ifort setting LDFLAGS... setting AR... ar setting ARFLAGS... ruv setting ARFLAGS_DYNAMIC...ruv checking whether make sets $(MAKE)... yes checking whether Fortran files must be preprocessed... no checking how to get verbose linking output from ifort... -v checking for Fortran libraries of ifort... -L/opt/intel/fc/10.1.012/lib -L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/32 -L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/32/.. -L/usr/lib -lifport -lifcore -limf -lm -lipgo -lirc -lgcc_s -lirc_s -ldl checking for dummy main to link with Fortran libraries... none checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore checking for library containing dgemm... no in /opt/intel/mkl/10.0.1.014/lib/em64t: checking for library containing dgemm... no in /opt/intel/mkl*/lib/em64t: checking for library containing dgemm... no in /opt/intel/cc/10.1.015/lib: checking for library containing dgemm... no in /opt/intel/fc/10.1.012/lib: checking for library containing dgemm... no checking for library containing dgemm... no in /usr/local/lib: checking for library containing dgemm... no in /cineca/prod/intel/lib: checking for library containing dgemm... no in /opt/intel/cc/10.1.015/lib: checking for library containing dgemm... no in /opt/intel/fc/10.1.012/lib: checking for library containing dgemm... no checking for library containing dgemm... no in /usr/local/lib: checking for library containing dgemm... no in /cineca/prod/intel/lib: checking for library containing dgemm... no in /opt/intel/cc/10.1.015/lib: checking for library containing dgemm... no in /opt/intel/fc/10.1.012/lib: checking for library containing dgemm... no checking for library containing zggev... no in /usr/local/lib: checking for library containing zggev... no in /cineca/prod/intel/lib: checking for library containing zggev... no in /opt/intel/cc/10.1.015/lib: checking for library containing zggev... no in /opt/intel/fc/10.1.012/lib: checking for library containing zggev... no setting BLAS_LIBS... ../flib/blas.a setting LAPACK_LIBS... ../flib/lapack.a checking for library containing fftwnd... no in /usr/local/lib: checking for library containing fftwnd... no in /cineca/prod/intel/lib: checking for library containing fftwnd... no in /opt/intel/cc/10.1.015/lib: checking for library containing fftwnd... no in /opt/intel/fc/10.1.012/lib: checking for library containing fftwnd... no setting FFT_LIBS... checking for library containing fftwnd... (cached) no setting MASS_LIBS... checking for library containing mpi_init... no setting MPI_LIBS... checking for library containing mpi_init... (cached) no setting DFLAGS... -D__INTEL -D__FFTW -D__USE_INTERNAL_FFTW setting IFLAGS... -I../include setting FDFLAGS... $(DFLAGS) checking for ranlib... ranlib setting RANLIB... ranlib configure: creating ./config.status config.status: creating include/fft_defs.h config.status: creating make.sys config.status: creating configure.msg config.status: creating include/c_defs.h config.status: include/c_defs.h is unchanged -------------------------------------------------------------------- ESPRESSO can take advantage of several optimized numerical libraries (essl, fftw, mkl...). This configure script attempts to find them, but may fail if they have been installed in non-standard locations. If a required library is not found, the local copy will be compiled. The following libraries have been found: BLAS_LIBS=../flib/blas.a LAPACK_LIBS=../flib/lapack.a FFT_LIBS= Please check if this is what you expect. If any libraries are missing, you may specify a list of directories to search and retry, as follows: ./configure LIBDIRS="list of directories, separated by spaces" Parallel environment not detected (is this a parallel machine?). Configured for compilation of serial executables. For more info, read the ESPRESSO User's Guide (Doc/users-guide.tex). -------------------------------------------------------------------- configure: success [phy at localhost espresso4.0cvs2]$ regards Sagar Bollywood, fun, friendship, sports and more. You name it, we have it on http://in.promos.yahoo.com/groups/bestofyahoo/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080517/1b161c41/attachment-0001.htm From sagarambavale at yahoo.co.in Sat May 17 15:19:20 2008 From: sagarambavale at yahoo.co.in (ambavale sagar) Date: Sat, 17 May 2008 18:49:20 +0530 (IST) Subject: [Pw_forum] acml-mkl Message-ID: <583075.38950.qm@web94608.mail.in2.yahoo.com> Dear Axel,O.Baris Malcioglu, Eduardo and all Thank you very much. I got that point. Yes it was ifort-32 which was making problem. Now for ifort-64 it is working. Now, I will try for acml on another system. It is great to have help from such nice and knowledgable persons. Hope in future I will be able to help others too. Thank you. Sagar BMR - a key player in weight issues. Know more - http://in.search.yahoo.com/search?&fr=na_onnetwork_mail_taglines&ei=UTF-8&rd=r1&p=basal+metabolic+rate -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080517/707371fb/attachment.htm From giannozz at nest.sns.it Mon May 19 11:28:09 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 19 May 2008 11:28:09 +0200 Subject: [Pw_forum] problem with neb calculation In-Reply-To: <2ebe300a0805160850n38597684icabd3b61240f5ed@mail.gmail.com> References: <20051007144345.62427.qmail@web60312.mail.yahoo.com> <43468F03.000005.25318@soapbox.yandex.ru> <2ebe300a0805160816o2627769fqa152b6eb96e2dd5b@mail.gmail.com> <25053.147.122.5.216.1210952095.squirrel@webmail.sissa.it> <2ebe300a0805160850n38597684icabd3b61240f5ed@mail.gmail.com> Message-ID: <48314829.1080803@nest.sns.it> Lucas Fernandez Seivane wrote: > compiling espresso 4.0 on a ppc64 linux cluster, and I have a well > known problem about ZHPEV. the problem is well known, so is the solution: if you use IBM ESSL (-D__ESSL) you need to load essl before lapack, as explained in file make.sys. If you use a version of ESSL that has standard calls for DSPEV and ZHPEV (as in some weird machines), use -D__LINUX_ESSL instead. > I am able to generate a nice pw.x, that works fine for many things > but not for the example25 [..] > ** On entry to ZHPEV parameter number 1 had an illegal value this sounds unlikely. Please find which call causes the problem. Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at nest.sns.it Mon May 19 11:30:20 2008 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 19 May 2008 11:30:20 +0200 Subject: [Pw_forum] About nelec and tot_charge again In-Reply-To: <882635.16279.qm@web73013.mail.tp2.yahoo.com> References: <882635.16279.qm@web73013.mail.tp2.yahoo.com> Message-ID: <483148AC.9010402@nest.sns.it> ? ?? wrote: > I heard there is a method call "Rigid Band > Approximation"(RBA). In order to shift Fermi level to > conduction band or valence band in semiconductor, does > it make sense just set "nelec" parameter only ? it does (in the limits of the RBA, of course) Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From eyvaz_isaev at yahoo.com Mon May 19 15:11:58 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 19 May 2008 06:11:58 -0700 (PDT) Subject: [Pw_forum] modification of phonon programs In-Reply-To: Message-ID: <777919.91083.qm@web65702.mail.ac4.yahoo.com> Dear developers, As I am mostly involved in phonon calculations and I have either not very good computers or time limitation per job on supercomputers I have an access I introduced some changes to phonon programs so that now one can specify iq_start and iq_end keywords in ph.in file to calculate phonons for a given set of q-points from dyn0-file. If this sounds interesting I can send these modified files. Bests, Eyvaz ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com From konstantin_kudin at yahoo.com Mon May 19 21:09:28 2008 From: konstantin_kudin at yahoo.com (Konstantin Kudin) Date: Mon, 19 May 2008 12:09:28 -0700 (PDT) Subject: [Pw_forum] modification of phonon programs In-Reply-To: <777919.91083.qm@web65702.mail.ac4.yahoo.com> Message-ID: <398294.19831.qm@web57704.mail.re3.yahoo.com> Dear Eyvaz, Is your option conceptually different from this commit: http://www.democritos.it:8888/O-sesame/chngview?cn=5136 "Added new input variables (iq1, iq2, iq3) to the PH code such that it is now possible to run the PH code for just one k point out of the full dispersion grid (specified by nq1, nq2, nq3). This way there is no need to run PW with 'phonon' first for a non-Gamma k point, and perhaps, there are some other positive (or negative?) effects that I am not aware of." ? Kostya --- Eyvaz Isaev wrote: > Dear developers, > > As I am mostly involved in phonon calculations and I > have either not very good computers or time > limitation per job on supercomputers I have an access > I introduced some changes to phonon programs so that > now one can specify iq_start and iq_end keywords in > ph.in file to calculate phonons for a given set of > q-points from dyn0-file. > > If this sounds interesting I can send these modified > files. > > Bests, > Eyvaz > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Theoretical Physics Department, Moscow State Institute of Steel & > Alloys, Russia, > Department of Physics, Chemistry, and Biology (IFM), Linkoping > University, Sweden > Condensed Matter Theory Group, Uppsala University, Sweden > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From qmmmworkshop at vitae.cmm.upenn.edu Mon May 19 20:43:55 2008 From: qmmmworkshop at vitae.cmm.upenn.edu (CMM QM/MM Workshop) Date: Mon, 19 May 2008 14:43:55 -0400 (EDT) Subject: [Pw_forum] CFP: 3rd Annual CMM Workshop on QM/MM Simulations Message-ID: Dear Colleague. We cordially invite you to register for the: 3rd Annual CMM 'Users Meet Developers' Workshop on QM/MM Simulations August 21st to 23rd 2008 in Philadelphia, PA * Goals The primary goal of this annual workshop is to encourage communication between users and developers of different Quantum Mechanics / Molecular Mechanics (QM/MM) approaches and implementations. It is meant to be a forum to exchange ideas about solutions to common problems, demonstrate successes of QM/MM applications and to discuss ways to make QM/MM calculations more versatile and also more accessible for newcomers to the field. To this effect, we particularly invite active developers of QM/MM codes and experienced users. * Format The 2008 workshop is planned to consist of oral and poster presentations on current methods developments and applications of QM/MM simulations in an informal and collegial atmosphere. Previous CMM QM/MM workshops have also shown to be a good platform for graduate students and postdocs to present their work and get useful comments from a competent audience. The schedule will give a lot of room for discussions (1/3 of the time allocated for each oral presentation). We will start on Thursday, August 21st in the evening (8 pm) with a reception, there will be presentations and a poster session on Friday, August 22nd and we close on Saturday, August 23rd in the late afternoon after another round of presentations. * Special Note: QM/MM Symposium at ACS Fall Meeting 2008 in Philadelphia Please note that the CMM QM/MM workshop directly follows the 2008 ACS Fall Meeting (Aug 17-21) in Philadelphia. During the ACS meeting a QM/MM symposium sponsored by the COMP section has been put together by the organizers of the CMM QM/MM workshop. Several of the invited speakers at the ACS symposium have indicated to stay for the CMM workshop as well, and thus the workshop will offer a great opportunity to discuss with experts in the field in a less formal atmosphere. The final program of the ACS symposium is not yet available online, but a link to the QM/MM symposium program will be made available through the workshop homepage. * Cost and Financial Support The workshop is sponsored by the LRSM ( http://www.lrsm.upenn.edu/ ) and the Merck Research Laboratories ( http://www.merck.com/mrl/ ). To keep the administrative overhead low, we don't provide any individual financial support, but in turn there is _NO_ registration or conference fee, and for qualified participants we can provide accommodation support in the form of a block of (double occupancy) rooms at no cost in a hotel within walking distance to the Penn campus. For other participants we will negotiate a discounted rate at the conference hotel. * Registration, Contributions and Participation To register for participation simply send an e-mail to qmmmworkshop at cmm.chem.upenn.edu stating: - your full name and affiliation - your research interest (field of research, developer or user, which QM/MM package, level or experience) - whether you would like to contribute a full (30min) or a short (10min) oral presentation and/or a poster and a respective tentative title. - whether you want to apply for accommodation support (see above) or prefer to organize accommodation for yourself. The maximum number of participants and presenters is limited due to the available funding, the size of the lecture hall, and to maintain the informal atmosphere, which has proven to be important for effective discussions. Special preference will be given to participants that increase the diversity of presentations and represented QM/MM codes. * __Deadline__ Please respond until: __June 8th 2008__ Confirmation of your attendance will be sent out via e-mail as soon as possible and at the latest shortly after the deadline. * Venue and Program The workshop will be held on the campus of the University of Pennsylvania in the University City area of Philadelphia. Details of venue and a tentative program will be published on the workshop home page as they become available: http://www.cmm.upenn.edu/qmmm2008.html The web page still contains the details for previous workshops (for your information) and will be updated continuously. * Contact If you have any questions about the workshop or the details of the organization please don't hesitate to contact us at: qmmmworkshop at cmm.chem.upenn.edu We are hoping to meet you soon in Philadelphia. On behalf of the CMM and the organizers, Axel Kohlmeyer. 2008/05/19 -- ======================================================================= Dr. Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu Associate Director - Center for Molecular Modeling - U. of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, http://www.cmm.upenn.edu ======================================================================= From eyvaz_isaev at yahoo.com Mon May 19 23:51:34 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 19 May 2008 14:51:34 -0700 (PDT) Subject: [Pw_forum] modification of phonon programs In-Reply-To: <398294.19831.qm@web57704.mail.re3.yahoo.com> Message-ID: <99126.4532.qm@web65712.mail.ac4.yahoo.com> Dear Kostya, I apologize, I did not understand the meaning of these variables you introduced. Can you please give more insight for these variables? What I did, in fact, very simple and hopefully, simple for users. I.e. one can restart dynamical matrix calculations from an interrupted q-point or for selected q-points from dyn0. In this way one can choose iq_start=5 as example, but it is possible to calculate dynamical matrices for selected q-points using iq_start=3 and iq_end=7. Of course, one can "parallelize" dynamical matrix calculations in this way. Of course, I am aware of iq_start keyword in PH, but supercomputers I use prefer saving temporary files in local/scratch directories (which then will be cleaned). That was a reason why I decided to modify the code. Bests, Eyvaz. --- Konstantin Kudin wrote: > Dear Eyvaz, > > Is your option conceptually different from this > commit: > http://www.democritos.it:8888/O-sesame/chngview?cn=5136 > > "Added new input variables (iq1, iq2, iq3) to the PH > code such that it > is now possible to run the PH code for just one k > point out of the full > dispersion grid (specified by nq1, nq2, nq3). This > way there is no need > to run PW with 'phonon' first for a non-Gamma k > point, and perhaps, > there are some other positive (or negative?) effects > that I am not > aware of." > > ? > > Kostya > > --- Eyvaz Isaev wrote: > > > Dear developers, > > > > As I am mostly involved in phonon calculations and > I > > have either not very good computers or time > > limitation per job on supercomputers I have an > access > > I introduced some changes to phonon programs so > that > > now one can specify iq_start and iq_end keywords > in > > ph.in file to calculate phonons for a given set of > > q-points from dyn0-file. > > > > If this sounds interesting I can send these > modified > > files. > > > > Bests, > > Eyvaz > > > > > ------------------------------------------------------------------- > > Prof. Eyvaz Isaev, > > Theoretical Physics Department, Moscow State > Institute of Steel & > > Alloys, Russia, > > Department of Physics, Chemistry, and Biology > (IFM), Linkoping > > University, Sweden > > Condensed Matter Theory Group, Uppsala University, > Sweden > > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, > eyvaz_isaev at yahoo.com > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com From eyvaz_isaev at yahoo.com Tue May 20 01:26:15 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 19 May 2008 16:26:15 -0700 (PDT) Subject: [Pw_forum] modification of phonon programs In-Reply-To: <99126.4532.qm@web65712.mail.ac4.yahoo.com> Message-ID: <414389.44842.qm@web65714.mail.ac4.yahoo.com> > Of course, I am aware of iq_start keyword in PH, but > supercomputers I use prefer saving temporary files > in local/scratch directories (which then will be > cleaned). Sorry, I have mistaken here. There is no iq_start keyword in ph.in file, but there is "recover" option. iq_start is used in phonon.f90 and phq_readin.f90 files. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com From coldwind1978 at yahoo.com.cn Tue May 20 13:46:02 2008 From: coldwind1978 at yahoo.com.cn (=?gb2312?q?=D5=EB=D2=B6=20=D6=EC?=) Date: Tue, 20 May 2008 19:46:02 +0800 (CST) Subject: [Pw_forum] ??? what's the meaning of error in compiler of sun In-Reply-To: Message-ID: <770075.36390.qm@web15803.mail.cnb.yahoo.com> Dear user: Thank you give some suggestions about compilation in solaris 9.0. The condition of my machine is as following : Sun fire 4800 and solaris sparc.I have install Sunstudio 12 in my machine. making ./configure is well done. When make pw, the errors appears. Please tell me how to modify my system. which development packages should be installed in my system to make successfully? Regards zhuzhenye pw_forum-request at pwscf.org ??? Send Pw_forum mailing list submissions to pw_forum at pwscf.org To subscribe or unsubscribe via the World Wide Web, visit http://www.democritos.it/mailman/listinfo/pw_forum or, via email, send a message with subject or body 'help' to pw_forum-request at pwscf.org You can reach the person managing the list at pw_forum-owner at pwscf.org When replying, please edit your Subject line so it is more specific than "Re: Contents of Pw_forum digest..." Today's Topics: 1. DOS Units (Vidur Parkash) 2. Re: DOS Units (lan haiping) 3. polarization calculation in ferroelectrics (hania djani-ait aissa) 4. Re: bug report in PWCOND (Dal Corso Andrea) 5. Re: acml - mkl (Lorenzo Paulatto) 6. Re: Starting magnetization (Lorenzo Paulatto) 7. Re: what's the meaning of error in compiler of sun solaris? (Lorenzo Paulatto) 8. ??? what's the meaning of error in compiler of sun solaris? (?? ?) 9. Re: ??? what's the meaning of error in compiler of sun solaris? (lan haiping) ---------------------------------------------------------------------- Message: 1 Date: Thu, 15 May 2008 23:43:01 -0700 (PDT) From: Vidur Parkash Subject: [Pw_forum] DOS Units To: pw_forum at pwscf.org Message-ID: <290135.76297.qm at web35406.mail.mud.yahoo.com> Content-Type: text/plain; charset="iso-8859-1" A simple question In what units does dos.x return the values of density of states? Is it states / eV / m^3 or something else? Vidur Vidur Parkash Electrical & Computer Engineering Michigan Technological University 716 EERC, 1400 Townsend Drive Houghton, MI-49931, USA Tel: 1-906-487-0023 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080515/1dfaa65e/attachment-0001.htm ------------------------------ Message: 2 Date: Fri, 16 May 2008 14:56:15 +0800 From: "lan haiping" Subject: Re: [Pw_forum] DOS Units To: vparkash at mtu.edu, "PWSCF Forum" Message-ID: Content-Type: text/plain; charset="iso-8859-1" from dos.f90: ! Output: ! ! The total DOS (states/eV plotted vs E in eV) is written to file "fildos" regards, Hai-Ping On Fri, May 16, 2008 at 2:43 PM, Vidur Parkash wrote: > A simple question > > In what units does dos.x return the values of density of states? Is it > states / eV / m^3 or something else? > > Vidur > > > Vidur Parkash > Electrical & Computer Engineering > Michigan Technological University > 716 EERC, 1400 Townsend Drive > Houghton, MI-49931, USA > Tel: 1-906-487-0023 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080516/a7344318/attachment-0001.htm ------------------------------ Message: 3 Date: Fri, 16 May 2008 06:51:12 +0000 From: hania djani-ait aissa Subject: [Pw_forum] polarization calculation in ferroelectrics To: Message-ID: Content-Type: text/plain; charset="iso-8859-1" Dear all, I am new PWSCF user, I am trying to calculate polarization in Bi4Ti3O12. this material is centered tetragonal in its paraelectric phase and orthorhombic bases centered in its ferroelectric one. having in mind the papers of Resta, King-smith and Vanderbilt, i have to fix the initial state with P=0 and then make a small displacement of a subgroup with respect to others. my question is: what will be the initial structure to put as input? the paraelectric tetragonal one with its symmetry center, or the ferroelectric one were i force the orthorhombic structure to be centered , relaxing all atoms and making the small displacement?? thank you in advance, Hania H. Djani Ait Aissa Center of Development of Advanced Technologies Haouch Oukil, PoBox.017, Algiers, Algeria _________________________________________________________________ Appelez vos amis de PC ? PC -- C'EST GRATUIT http://get.live.com/messenger/overview ------------------------------ Message: 4 Date: Fri, 16 May 2008 09:08:33 +0200 From: Dal Corso Andrea Subject: Re: [Pw_forum] bug report in PWCOND To: PWSCF Forum Message-ID: <1210921713.3353.2.camel at dhpc-5-03.sissa.it> Content-Type: text/plain Dear Zhiping, You are right, thank you. I will correct the cvs version. Andrea Dal Corso On Thu, 2008-05-15 at 19:05 -0500, zx3 at rice.edu wrote: > Dear all: > In CVS_080208 and previous version, File: PWCOND/local.f90 > Line 410: > ------------------------------------------------------------- > INTEGER :: nrx, nry, fftxy(-nrx:nrx, -nrx:nry), & > number, n1, n2 > ------------------------------------------------------------- > should be > ------------------------------------------------------------- > INTEGER :: nrx, nry, fftxy(-nrx:nrx, -nry:nry), & > number, n1, n2 > ------------------------------------------------------------- > where -nry was mistyped as -nrx > Best, > Zhiping > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Andrea Dal Corso Tel. 0039-040-3787428 SISSA, Via Beirut 2/4 Fax. 0039-040-3787528 34014 Trieste (Italy) e-mail: dalcorso at sissa.it ------------------------------ Message: 5 Date: Fri, 16 May 2008 09:34:45 +0200 (CEST) From: "Lorenzo Paulatto" Subject: Re: [Pw_forum] acml - mkl To: "PWSCF Forum" Message-ID: <14099.79.1.239.82.1210923285.squirrel at webmail.sissa.it> Content-Type: text/plain;charset=iso-8859-1 On Thu, May 15, 2008 19:36, Eduardo Ariel Menendez Proupin wrote: > the operating system has a strange architecture x86_64 (as given by the > command uname -a), but the As far as I know, x86_64 is the standard name for 64bit architectures AMD64 and Intel64 (not itanium). -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) +39 040 3787 511 http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ ------------------------------ Message: 6 Date: Fri, 16 May 2008 09:40:39 +0200 (CEST) From: "Lorenzo Paulatto" Subject: Re: [Pw_forum] Starting magnetization To: "Axel Kohlmeyer" , "PWSCF Forum" Message-ID: <14173.79.1.239.82.1210923639.squirrel at webmail.sissa.it> Content-Type: text/plain;charset=iso-8859-1 On Thu, May 15, 2008 20:53, Axel Kohlmeyer wrote: > yes. the parameter ntypx determins the maximum number > of atom type entries. it is set in Modules/parameters.f90 > and the default value is 10. In version 4.0 there only a few (maybe zero), static arrays of size ntyp. I think we could have removed that limit for the next release, but there is not enough time now. It will be done for 4.1 bye -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) +39 040 3787 511 http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ ------------------------------ Message: 7 Date: Fri, 16 May 2008 09:44:21 +0200 (CEST) From: "Lorenzo Paulatto" Subject: Re: [Pw_forum] what's the meaning of error in compiler of sun solaris? To: "PWSCF Forum" Message-ID: <14222.79.1.239.82.1210923861.squirrel at webmail.sissa.it> Content-Type: text/plain;charset=iso-8859-1 On Fri, May 16, 2008 04:01, ???? ?? wrote: > what is the meaning of the error, and how to deal with it? Please give > me some suggestios. Dear Zhuzhenye, you could have provided a few more lines to help us figure out what is going on. From what I can see, it looks like you are missing some basic development libraries. I'm no Solaris guru, but I can imagine there are some development packages you can install in the system. Have you checked they are actually installed? regards P.S. please provide your affiliation when writing to this mailing list -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) +39 040 3787 511 http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ ------------------------------ Message: 8 Date: Fri, 16 May 2008 18:54:46 +0800 (CST) From: ?? ? Subject: [Pw_forum] ??? what's the meaning of error in compiler of sun solaris? To: pw_forum at pwscf.org Message-ID: <423629.23615.qm at web15807.mail.cnb.yahoo.com> Content-Type: text/plain; charset="gb2312" ?????????? --------------------------------- ???????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080516/2cb55a5b/attachment-0001.htm -------------- next part -------------- An embedded message was scrubbed... From: =?gb2312?q?=D5=EB=D2=B6=20=D6=EC?= Subject: what's the meaning of error in compiler of sun solaris? Date: Fri, 16 May 2008 10:01:14 +0800 (CST) Size: 2763 Url: http://www.democritos.it/pipermail/pw_forum/attachments/20080516/2cb55a5b/attachment-0001.eml ------------------------------ Message: 9 Date: Fri, 16 May 2008 19:25:46 +0800 From: "lan haiping" Subject: Re: [Pw_forum] ??? what's the meaning of error in compiler of sun solaris? To: "PWSCF Forum" Message-ID: Content-Type: text/plain; charset="gb2312" Why do you repeat your email's content ? This is a mail-list, and every thread will be kept. Just forwarding your previous mail to this mai-list won't help your problem solve . You should give more detailed compilation environments 2008/5/16 ?? ? : > > > ?????????? > > ------------------------------ > ???????????? > > ---------- Forwarded message ---------- > From: ?? ? > To: pw_forum at pwscf.org > Date: Fri, 16 May 2008 10:01:14 +0800 (CST) > Subject: what's the meaning of error in compiler of sun solaris? > Dear users: > I want to compile pwscf in sun solaris 9.0. when i make pw, the error > appears as following: > ld: fatal: Symbol referencing errors. No output written to > pw.x > *** Error code 1 > make: Fatal error: Command failed for target `pw.x' > Current working directory /zzy/espresso-4.0/PW > *** Error code 1 > make: Fatal error: Command failed for target `pw' > what is the meaning of the error, and how to deal with it? Please give me > some suggestios. > > Regards > > zhuzhenye > > > ------------------------------ > ???????????? > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080516/9b646261/attachment.htm ------------------------------ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum End of Pw_forum Digest, Vol 11, Issue 24 **************************************** --------------------------------- ???????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080520/b5f2f008/attachment.htm From coldwind1978 at yahoo.com.cn Tue May 20 13:46:05 2008 From: coldwind1978 at yahoo.com.cn (=?gb2312?q?=D5=EB=D2=B6=20=D6=EC?=) Date: Tue, 20 May 2008 19:46:05 +0800 (CST) Subject: [Pw_forum] ??? what's the meaning of error in compiler of sun In-Reply-To: Message-ID: <796810.2503.qm@web15804.mail.cnb.yahoo.com> Dear user: Thank you give some suggestions about compilation in solaris 9.0. The condition of my machine is as following : Sun fire 4800 and solaris sparc.I have install Sunstudio 12 in my machine. making ./configure is well done. When make pw, the errors appears. Please tell me how to modify my system. which development packages should be installed in my system to make successfully? Regards zhuzhenye pw_forum-request at pwscf.org ??? Send Pw_forum mailing list submissions to pw_forum at pwscf.org To subscribe or unsubscribe via the World Wide Web, visit http://www.democritos.it/mailman/listinfo/pw_forum or, via email, send a message with subject or body 'help' to pw_forum-request at pwscf.org You can reach the person managing the list at pw_forum-owner at pwscf.org When replying, please edit your Subject line so it is more specific than "Re: Contents of Pw_forum digest..." Today's Topics: 1. DOS Units (Vidur Parkash) 2. Re: DOS Units (lan haiping) 3. polarization calculation in ferroelectrics (hania djani-ait aissa) 4. Re: bug report in PWCOND (Dal Corso Andrea) 5. Re: acml - mkl (Lorenzo Paulatto) 6. Re: Starting magnetization (Lorenzo Paulatto) 7. Re: what's the meaning of error in compiler of sun solaris? (Lorenzo Paulatto) 8. ??? what's the meaning of error in compiler of sun solaris? (?? ?) 9. Re: ??? what's the meaning of error in compiler of sun solaris? (lan haiping) ---------------------------------------------------------------------- Message: 1 Date: Thu, 15 May 2008 23:43:01 -0700 (PDT) From: Vidur Parkash Subject: [Pw_forum] DOS Units To: pw_forum at pwscf.org Message-ID: <290135.76297.qm at web35406.mail.mud.yahoo.com> Content-Type: text/plain; charset="iso-8859-1" A simple question In what units does dos.x return the values of density of states? Is it states / eV / m^3 or something else? Vidur Vidur Parkash Electrical & Computer Engineering Michigan Technological University 716 EERC, 1400 Townsend Drive Houghton, MI-49931, USA Tel: 1-906-487-0023 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080515/1dfaa65e/attachment-0001.htm ------------------------------ Message: 2 Date: Fri, 16 May 2008 14:56:15 +0800 From: "lan haiping" Subject: Re: [Pw_forum] DOS Units To: vparkash at mtu.edu, "PWSCF Forum" Message-ID: Content-Type: text/plain; charset="iso-8859-1" from dos.f90: ! Output: ! ! The total DOS (states/eV plotted vs E in eV) is written to file "fildos" regards, Hai-Ping On Fri, May 16, 2008 at 2:43 PM, Vidur Parkash wrote: > A simple question > > In what units does dos.x return the values of density of states? Is it > states / eV / m^3 or something else? > > Vidur > > > Vidur Parkash > Electrical & Computer Engineering > Michigan Technological University > 716 EERC, 1400 Townsend Drive > Houghton, MI-49931, USA > Tel: 1-906-487-0023 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080516/a7344318/attachment-0001.htm ------------------------------ Message: 3 Date: Fri, 16 May 2008 06:51:12 +0000 From: hania djani-ait aissa Subject: [Pw_forum] polarization calculation in ferroelectrics To: Message-ID: Content-Type: text/plain; charset="iso-8859-1" Dear all, I am new PWSCF user, I am trying to calculate polarization in Bi4Ti3O12. this material is centered tetragonal in its paraelectric phase and orthorhombic bases centered in its ferroelectric one. having in mind the papers of Resta, King-smith and Vanderbilt, i have to fix the initial state with P=0 and then make a small displacement of a subgroup with respect to others. my question is: what will be the initial structure to put as input? the paraelectric tetragonal one with its symmetry center, or the ferroelectric one were i force the orthorhombic structure to be centered , relaxing all atoms and making the small displacement?? thank you in advance, Hania H. Djani Ait Aissa Center of Development of Advanced Technologies Haouch Oukil, PoBox.017, Algiers, Algeria _________________________________________________________________ Appelez vos amis de PC ? PC -- C'EST GRATUIT http://get.live.com/messenger/overview ------------------------------ Message: 4 Date: Fri, 16 May 2008 09:08:33 +0200 From: Dal Corso Andrea Subject: Re: [Pw_forum] bug report in PWCOND To: PWSCF Forum Message-ID: <1210921713.3353.2.camel at dhpc-5-03.sissa.it> Content-Type: text/plain Dear Zhiping, You are right, thank you. I will correct the cvs version. Andrea Dal Corso On Thu, 2008-05-15 at 19:05 -0500, zx3 at rice.edu wrote: > Dear all: > In CVS_080208 and previous version, File: PWCOND/local.f90 > Line 410: > ------------------------------------------------------------- > INTEGER :: nrx, nry, fftxy(-nrx:nrx, -nrx:nry), & > number, n1, n2 > ------------------------------------------------------------- > should be > ------------------------------------------------------------- > INTEGER :: nrx, nry, fftxy(-nrx:nrx, -nry:nry), & > number, n1, n2 > ------------------------------------------------------------- > where -nry was mistyped as -nrx > Best, > Zhiping > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Andrea Dal Corso Tel. 0039-040-3787428 SISSA, Via Beirut 2/4 Fax. 0039-040-3787528 34014 Trieste (Italy) e-mail: dalcorso at sissa.it ------------------------------ Message: 5 Date: Fri, 16 May 2008 09:34:45 +0200 (CEST) From: "Lorenzo Paulatto" Subject: Re: [Pw_forum] acml - mkl To: "PWSCF Forum" Message-ID: <14099.79.1.239.82.1210923285.squirrel at webmail.sissa.it> Content-Type: text/plain;charset=iso-8859-1 On Thu, May 15, 2008 19:36, Eduardo Ariel Menendez Proupin wrote: > the operating system has a strange architecture x86_64 (as given by the > command uname -a), but the As far as I know, x86_64 is the standard name for 64bit architectures AMD64 and Intel64 (not itanium). -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) +39 040 3787 511 http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ ------------------------------ Message: 6 Date: Fri, 16 May 2008 09:40:39 +0200 (CEST) From: "Lorenzo Paulatto" Subject: Re: [Pw_forum] Starting magnetization To: "Axel Kohlmeyer" , "PWSCF Forum" Message-ID: <14173.79.1.239.82.1210923639.squirrel at webmail.sissa.it> Content-Type: text/plain;charset=iso-8859-1 On Thu, May 15, 2008 20:53, Axel Kohlmeyer wrote: > yes. the parameter ntypx determins the maximum number > of atom type entries. it is set in Modules/parameters.f90 > and the default value is 10. In version 4.0 there only a few (maybe zero), static arrays of size ntyp. I think we could have removed that limit for the next release, but there is not enough time now. It will be done for 4.1 bye -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) +39 040 3787 511 http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ ------------------------------ Message: 7 Date: Fri, 16 May 2008 09:44:21 +0200 (CEST) From: "Lorenzo Paulatto" Subject: Re: [Pw_forum] what's the meaning of error in compiler of sun solaris? To: "PWSCF Forum" Message-ID: <14222.79.1.239.82.1210923861.squirrel at webmail.sissa.it> Content-Type: text/plain;charset=iso-8859-1 On Fri, May 16, 2008 04:01, ???? ?? wrote: > what is the meaning of the error, and how to deal with it? Please give > me some suggestios. Dear Zhuzhenye, you could have provided a few more lines to help us figure out what is going on. From what I can see, it looks like you are missing some basic development libraries. I'm no Solaris guru, but I can imagine there are some development packages you can install in the system. Have you checked they are actually installed? regards P.S. please provide your affiliation when writing to this mailing list -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) +39 040 3787 511 http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ ------------------------------ Message: 8 Date: Fri, 16 May 2008 18:54:46 +0800 (CST) From: ?? ? Subject: [Pw_forum] ??? what's the meaning of error in compiler of sun solaris? To: pw_forum at pwscf.org Message-ID: <423629.23615.qm at web15807.mail.cnb.yahoo.com> Content-Type: text/plain; charset="gb2312" ?????????? --------------------------------- ???????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080516/2cb55a5b/attachment-0001.htm -------------- next part -------------- An embedded message was scrubbed... From: =?gb2312?q?=D5=EB=D2=B6=20=D6=EC?= Subject: what's the meaning of error in compiler of sun solaris? Date: Fri, 16 May 2008 10:01:14 +0800 (CST) Size: 2763 Url: http://www.democritos.it/pipermail/pw_forum/attachments/20080516/2cb55a5b/attachment-0001.eml ------------------------------ Message: 9 Date: Fri, 16 May 2008 19:25:46 +0800 From: "lan haiping" Subject: Re: [Pw_forum] ??? what's the meaning of error in compiler of sun solaris? To: "PWSCF Forum" Message-ID: Content-Type: text/plain; charset="gb2312" Why do you repeat your email's content ? This is a mail-list, and every thread will be kept. Just forwarding your previous mail to this mai-list won't help your problem solve . You should give more detailed compilation environments 2008/5/16 ?? ? : > > > ?????????? > > ------------------------------ > ???????????? > > ---------- Forwarded message ---------- > From: ?? ? > To: pw_forum at pwscf.org > Date: Fri, 16 May 2008 10:01:14 +0800 (CST) > Subject: what's the meaning of error in compiler of sun solaris? > Dear users: > I want to compile pwscf in sun solaris 9.0. when i make pw, the error > appears as following: > ld: fatal: Symbol referencing errors. No output written to > pw.x > *** Error code 1 > make: Fatal error: Command failed for target `pw.x' > Current working directory /zzy/espresso-4.0/PW > *** Error code 1 > make: Fatal error: Command failed for target `pw' > what is the meaning of the error, and how to deal with it? Please give me > some suggestios. > > Regards > > zhuzhenye > > > ------------------------------ > ???????????? > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080516/9b646261/attachment.htm ------------------------------ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum End of Pw_forum Digest, Vol 11, Issue 24 **************************************** --------------------------------- ???????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080520/79b9a6f7/attachment-0001.htm From giannozz at democritos.it Tue May 20 14:27:36 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 20 May 2008 14:27:36 +0200 Subject: [Pw_forum] ??? what's the meaning of error in compiler of sun In-Reply-To: <770075.36390.qm@web15803.mail.cnb.yahoo.com> References: <770075.36390.qm@web15803.mail.cnb.yahoo.com> Message-ID: <4832C3B8.6060701@democritos.it> ?? ? wrote: > Thank you give some suggestions about compilation in solaris 9.0. The > condition of my machine is as following : Sun fire 4800 and solaris > sparc.I have install Sunstudio 12 in my machine. making ./configure is > well done. When make pw, the errors appears. which errors? -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Tue May 20 15:24:08 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 20 May 2008 15:24:08 +0200 Subject: [Pw_forum] modification of phonon programs In-Reply-To: <777919.91083.qm@web65702.mail.ac4.yahoo.com> References: <777919.91083.qm@web65702.mail.ac4.yahoo.com> Message-ID: <4832D0F8.6030406@democritos.it> Eyvaz Isaev wrote: > I introduced some changes to phonon programs so that > now one can specify iq_start and iq_end keywords in > ph.in file to calculate phonons for a given set of > q-points from dyn0-file. > > If this sounds interesting I can send these modified files. it is interesting, but it is just part of the story. The phonon code presently uses only pools of processors, for k-point and plane-wave parallelization. There are however two more possible "cheap" parallelizations: over irreps, and over q-vectors. Both involve loosely coupled calculations that can be performed almost independently and thus are ideally suited for a "Grid computing" environment. Rather than via MPI calls, parallelization could be achieved by a script distributing the various calculations across many jobs, collecting the results again with a script or with an auxiliary code reading the outputd data file. This will require some changes to both the input data and the data files, but nothing dramatic. There are already two methods to supply a single q-point: the one described by Kostantin Kudin, and directly as qx, qy, qz. Both may require in the future to be modified, in order to better fit into the above picture. Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Tue May 20 15:28:32 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 20 May 2008 15:28:32 +0200 Subject: [Pw_forum] electron phonon coupling / cannot remap grid on k-point list error In-Reply-To: <899166.36606.qm@web82003.mail.mud.yahoo.com> References: <899166.36606.qm@web82003.mail.mud.yahoo.com> Message-ID: <4832D200.7070109@democritos.it> hamad mohamed wrote: > error message > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > cannot remap grid on k-point list > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > is a peering by performing the electron phonon coupling for a > tetragonal body center unit cell, where the meshes are: > > dense 24 24 24 0 0 0 > rare 2 2 2 0 0 0 > phonon 2 2 1 > > where all the division of nk and nq that correspond to dense/rare , > dense/phonon and rare/phonon are integer. was it too much work to provide a test job? -- Paolo Giannozzi, Democritos and University of Udine, Italy From yu.xie at mat.ethz.ch Wed May 21 15:46:14 2008 From: yu.xie at mat.ethz.ch (Yu Xie) Date: Wed, 21 May 2008 15:46:14 +0200 Subject: [Pw_forum] Compile pwscf on HP Unix Message-ID: Dear PWSCF users, I'm trying to install the pwscf 3.2.3 on a HP Unix machine. The compiler is f90. And I got some problems with compute_fes_grads.F90. The error message is like below: cpp -P -traditional -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI - D__PARA -I../include compute_fes_grads.f90 -o compute_fes_grads.F90 mpif90 -O -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA - I../include -I./ -I../Modules -I../iotk/src -I../PW -I../PH -I../ CPV -c compute_fes_grads.F90 -o compute_fes_grads.o /var/tmp//fciBAAa21392.F90 external subroutine COMPUTE_FES_GRADS internal subroutine WRITE_RESTART internal function INTERRUPT_RUN Error 1055 : In program unit COMPUTE_FES_GRADS variable STARTINGPOT has not been given a type Error 1055 : In program unit COMPUTE_FES_GRADS variable STARTINGWFC has not been given a type external subroutine METADYN internal subroutine FREE_ENERGY_GRAD internal subroutine MOVE_TO_TARGET dirname = TRIM( tmp_dir ) // TRIM( prefix ) // '.save' ^ Warning 441 at (502:compute_fes_grads.F90) : Character string truncated to length 256 on assignment external subroutine RESET_INIT_MAG external subroutine ELECTRONIC_SCF 2 Errors f90: error 213: Errors detected. *** Error exit code 1 Stop. *** Error exit code 1 Stop. How can I correct this error? Thanks very much! With mu best regards, Yu From akohlmey at cmm.chem.upenn.edu Wed May 21 16:13:01 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 21 May 2008 10:13:01 -0400 (EDT) Subject: [Pw_forum] Compile pwscf on HP Unix In-Reply-To: References: Message-ID: On Wed, 21 May 2008, Yu Xie wrote: YX> Dear PWSCF users, dear yu, without looking much into details i have three suggestions: 1) you should update to the brand new and much improved version 4.0 2) you should see whether your compiler is up-to-date. that code has been compiled successfully by a large number of people with quite diverse compilers, so it is likely that your compiler is at fault. 3) you should respect the policy of this mailing list to state your name and affiliation. cheers, axel. p.s.: they don't call it "HP-SUX" for nothing ... ;-) YX> YX> I'm trying to install the pwscf 3.2.3 on a HP Unix machine. The YX> compiler is f90. And I got some problems with compute_fes_grads.F90. YX> The error message is like below: YX> YX> cpp -P -traditional -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI - YX> D__PARA -I../include compute_fes_grads.f90 -o compute_fes_grads.F90 YX> mpif90 -O -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA - YX> I../include -I./ -I../Modules -I../iotk/src -I../PW -I../PH -I../ YX> CPV -c compute_fes_grads.F90 -o compute_fes_grads.o YX> /var/tmp//fciBAAa21392.F90 YX> external subroutine COMPUTE_FES_GRADS YX> internal subroutine WRITE_RESTART YX> internal function INTERRUPT_RUN YX> Error 1055 : In program unit COMPUTE_FES_GRADS variable STARTINGPOT YX> has not been given a type YX> Error 1055 : In program unit COMPUTE_FES_GRADS variable STARTINGWFC YX> has not been given a type YX> external subroutine METADYN YX> internal subroutine FREE_ENERGY_GRAD YX> internal subroutine MOVE_TO_TARGET YX> dirname = TRIM( tmp_dir ) // TRIM( prefix ) // '.save' YX> ^ YX> Warning 441 at (502:compute_fes_grads.F90) : Character string YX> truncated to length 256 on assignment YX> external subroutine RESET_INIT_MAG YX> external subroutine ELECTRONIC_SCF YX> YX> 2 Errors YX> f90: error 213: Errors detected. YX> *** Error exit code 1 YX> YX> Stop. YX> *** Error exit code 1 YX> YX> Stop. YX> YX> How can I correct this error? YX> YX> Thanks very much! YX> YX> With mu best regards, YX> YX> Yu YX> _______________________________________________ YX> Pw_forum mailing list YX> Pw_forum at pwscf.org YX> http://www.democritos.it/mailman/listinfo/pw_forum YX> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From giannozz at democritos.it Wed May 21 16:51:24 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 21 May 2008 16:51:24 +0200 Subject: [Pw_forum] Compile pwscf on HP Unix In-Reply-To: References: Message-ID: <483436EC.4000907@democritos.it> Yu Xie wrote: > I'm trying to install the pwscf 3.2.3 on a HP Unix machine. you should install the new 4.0 version instead (but it will not solve your problem). > Error 1055 : In program unit COMPUTE_FES_GRADS variable STARTINGPOT > has not been given a type > Error 1055 : In program unit COMPUTE_FES_GRADS variable STARTINGWFC > has not been given a type it looks like a compiler bug. More exactly: there is a weird usage, syntactically correct but very awkward, of variables STARTINGPOT and STARTINGWFC from two different modules,that confuses the compiler (it confuses me as well). A compiler that gets confused is buggy by definition. > How can I correct this error? not sure you can. It depends on the kind of machine yout have. Try to update your compiler to a more recent version, or to get a different compiler. Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From yu.xie at mat.ethz.ch Wed May 21 17:10:07 2008 From: yu.xie at mat.ethz.ch (Yu Xie) Date: Wed, 21 May 2008 17:10:07 +0200 Subject: [Pw_forum] Compile pwscf on HP Unix In-Reply-To: References: Message-ID: Dear Axel, Thanks for your advices. I followed your suggestions, and met with new errors: 1) I tried to compile the 4.0, it has error with bfgs_module.F90. The error message is addressed below: cpp -P -traditional -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI - D__PARA -I../include bfgs_module.f90 -o bfgs_module.F90 mpif90 -O -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA - I../include -I./ -I../Modules -I../iotk/src -I../PW -I../PH -c bfgs_module.F90 -o bfgs_module.o /var/tmp//fciBAAa08264.F90 module BFGS_MODULE module subroutine BFGS if (lmovecell) FORALL( i=1:3, j=1:3) pos( n-9 + j+3*(i-1) ) = h(i,j) ^ Error 724 at (205:bfgs_module.F90) : syntax error if (lmovecell) FORALL( i=1:3, j=1:3) grad( n-9 + j+3*(i-1) ) = fcell(i,j) ^ Error 724 at (208:bfgs_module.F90) : syntax error IF ( lmovecell ) FORALL( i=1:3, j=1:3) h(i,j) = pos( n-9 + j +3*(i-1) ) ^ Error 724 at (420:bfgs_module.F90) : syntax error internal subroutine GDIIS_STEP module subroutine RESET_BFGS module subroutine READ_BFGS_FILE module subroutine WRITE_BFGS_FILE module subroutine UPDATE_INVERSE_HESSIAN module subroutine CHECK_WOLFE_CONDITIONS module subroutine COMPUTE_TRUST_RADIUS module function SCNORM module subroutine TERMINATE_BFGS 3 Errors f90: error 213: Errors detected. *** Error exit code 1 Stop. *** Error exit code 1 However, I never met any problem when I compiled pwscf on Linux or MacOSX. So the problem would be the compiler. 2) I can't change anything of the machine which I want to use pwscf. I will suggest the technical support group to update the compiler. 3) OOOOH. I forgot it. Sorry!! Thanks again! Best regards, Yu On May 21, 2008, at 4:13 PM, Axel Kohlmeyer wrote: > On Wed, 21 May 2008, Yu Xie wrote: > > YX> Dear PWSCF users, > > > dear yu, > > without looking much into details i have three suggestions: > 1) you should update to the brand new and much improved version 4.0 > 2) you should see whether your compiler is up-to-date. that code has > been compiled successfully by a large number of people with quite > diverse compilers, so it is likely that your compiler is at fault. > 3) you should respect the policy of this mailing list to > state your name and affiliation. > > cheers, > axel. > > p.s.: they don't call it "HP-SUX" for nothing ... ;-) > > YX> > YX> I'm trying to install the pwscf 3.2.3 on a HP Unix machine. The > YX> compiler is f90. And I got some problems with > compute_fes_grads.F90. > YX> The error message is like below: > YX> > YX> cpp -P -traditional -D__FFTW -D__USE_INTERNAL_FFTW - > D__MPI - > YX> D__PARA -I../include compute_fes_grads.f90 -o > compute_fes_grads.F90 > YX> mpif90 -O -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI - > D__PARA - > YX> I../include -I./ -I../Modules -I../iotk/src -I../PW -I../ > PH -I../ > YX> CPV -c compute_fes_grads.F90 -o compute_fes_grads.o > YX> /var/tmp//fciBAAa21392.F90 > YX> external subroutine COMPUTE_FES_GRADS > YX> internal subroutine WRITE_RESTART > YX> internal function INTERRUPT_RUN > YX> Error 1055 : In program unit COMPUTE_FES_GRADS variable > STARTINGPOT > YX> has not been given a type > YX> Error 1055 : In program unit COMPUTE_FES_GRADS variable > STARTINGWFC > YX> has not been given a type > YX> external subroutine METADYN > YX> internal subroutine FREE_ENERGY_GRAD > YX> internal subroutine MOVE_TO_TARGET > YX> dirname = TRIM( tmp_dir ) // TRIM( prefix ) // '.save' > YX> ^ > YX> Warning 441 at (502:compute_fes_grads.F90) : Character string > YX> truncated to length 256 on assignment > YX> external subroutine RESET_INIT_MAG > YX> external subroutine ELECTRONIC_SCF > YX> > YX> 2 Errors > YX> f90: error 213: Errors detected. > YX> *** Error exit code 1 > YX> > YX> Stop. > YX> *** Error exit code 1 > YX> > YX> Stop. > YX> > YX> How can I correct this error? > YX> > YX> Thanks very much! > YX> > YX> With mu best regards, > YX> > YX> Yu > YX> _______________________________________________ > YX> Pw_forum mailing list > YX> Pw_forum at pwscf.org > YX> http://www.democritos.it/mailman/listinfo/pw_forum > YX> > > -- > = > ====================================================================== > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http:// > www.cmm.upenn.edu > Center for Molecular Modeling -- University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA > 19104-6323 > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 > = > ====================================================================== > If you make something idiot-proof, the universe creates a better > idiot. ============================================== Yu Xie Laboratory of Crystallography, Department of Material Science ETH Zurich, HCI G 504, Wolfgang-Pauli-Str. 10 CH-8093 Zurich Switzerland email: yu.xie at mat.ethz.ch tel: +41-44-6326542 fax: +41-44-6321133 ============================================== From anjmanqi at yahoo.com.cn Wed May 21 19:12:23 2008 From: anjmanqi at yahoo.com.cn (jiming an) Date: Thu, 22 May 2008 01:12:23 +0800 (CST) Subject: [Pw_forum] How to fix "occupations (j) wrong" Message-ID: <824480.9573.qm@web15007.mail.cnb.yahoo.com> Hi, all, I want to generate pseudo potential of Sb atom. Here are the input script and wrong message: -------------------------------------------------------------------------------------------------------- &input title='Sb', zed=51., rel=2, rlderiv=2.80, eminld=-5.0, emaxld=5.0, deld=0.02, nld=5, iswitch=3, config='[Kr] 5s2 4d10 5p3 ' dft='PBE', / &inputp pseudotype=3, lloc=1, rcloc=10.0, file_pseudopw='Sbrel.RRKJ3', / 7 4D 3 2 5.0 0.00 2.60 2.60 1.50 4D 3 2 0.0 0.00 2.6 2.6 1.50 4D 3 2 5.0 0.00 2.60 2.60 2.50 4D 3 2 0.0 0.00 2.6 2.6 2.50 5S 1 0 2.0 0.00 2.60 2.60 0.50 5P 2 1 2.0 0.00 2.60 2.60 0.50 5P 2 1 1.0 0.00 2.60 2.60 1.50 --------------------------------------------------------------------------------------------------------- program ld1 starts. version 3.2.3 today is 21May2008 at 13:26:23 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_psconfig : error # 1 occupations (j) wrong %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... --------------------------------------------------------------------------------------------------------------------------------------------------------- Ask Proficient to fix it, Thanks. Jiming An ___________________________________________________________ ???????????? http://cn.mail.yahoo.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080522/a4f43918/attachment.htm From baroni at sissa.it Wed May 21 19:42:40 2008 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 21 May 2008 19:42:40 +0200 Subject: [Pw_forum] How to fix "occupations (j) wrong" In-Reply-To: <824480.9573.qm@web15007.mail.cnb.yahoo.com> References: <824480.9573.qm@web15007.mail.cnb.yahoo.com> Message-ID: <6D6F49D0-BDE3-43B9-9AF3-29782B85539F@sissa.it> On May 21, 2008, at 7:12 PM, jiming an wrote: > Hi, all, > I want to generate pseudo potential of Sb atom. Here are the > input script and wrong message: > -------------------------------------------------------------------------------------------------------- .... > 7 > 4D 3 2 5.0 0.00 2.60 2.60 1.50 > 4D 3 2 0.0 0.00 2.6 2.6 1.50 > 4D 3 2 5.0 0.00 2.60 2.60 2.50 > 4D 3 2 0.0 0.00 2.6 2.6 2.50 > 5S 1 0 2.0 0.00 2.60 2.60 0.50 > 5P 2 1 2.0 0.00 2.60 2.60 0.50 > 5P 2 1 1.0 0.00 2.60 2.60 1.50 I may understand very little of the input syntax of the (present version of the) ld1 program, which I wrote long ago, but it seems to me that yours is rather weird: how it comes that you have four different input lines for 4d electrons and two for 5p ones? Shouldn't one line per atomic orbital be enough? Also, please do not forget to append your academic affiliation to posts to this mailing list SB --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080521/5baf0dbd/attachment-0001.htm From degironc at sissa.it Wed May 21 22:13:13 2008 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 21 May 2008 22:13:13 +0200 Subject: [Pw_forum] How to fix "occupations (j) wrong" In-Reply-To: <824480.9573.qm@web15007.mail.cnb.yahoo.com> References: <824480.9573.qm@web15007.mail.cnb.yahoo.com> Message-ID: <48348259.4010207@sissa.it> Dear Jiming An > 7 > 4D 3 2 5.0 0.00 2.60 2.60 1.50 > 4D 3 2 0.0 0.00 2.6 2.6 1.50 > 4D 3 2 5.0 0.00 2.60 2.60 2.50 > 4D 3 2 0.0 0.00 2.6 2.6 2.50 > 5S 1 0 2.0 0.00 2.60 2.60 0.50 > 5P 2 1 2.0 0.00 2.60 2.60 0.50 > 5P 2 1 1.0 0.00 2.60 2.60 1.50 in the fully relativistic case the maximum occupation of a level is determined by the value of J... so J=1.5 implies max occupation =4.0 and J=2.5 implies max occ = 6.0 hope it helps, stefano From anjmanqi at yahoo.com.cn Wed May 21 23:59:09 2008 From: anjmanqi at yahoo.com.cn (jiming an) Date: Thu, 22 May 2008 05:59:09 +0800 (CST) Subject: [Pw_forum] Why does the script of example As has two 4P rows and two 4Drows. Message-ID: <833102.6034.qm@web15002.mail.cnb.yahoo.com> Dear authors of pwscf: I want to generate Sb atom pseudo potential, so, I read the document and the examples carefully. Here is the script of example As: ------------------------------------------------------------------------------------------------------------------------------------ &input title='As', zed=33., rel=2, rlderiv=2.50, eminld=-4.0, emaxld=4.0, deld=0.02, nld=5, iswitch=3, config='[Ar] 3d10 4s2 4p3 4d-1' dft='LDA', / &inputp pseudotype=2, lloc=2, file_pseudopw='Asrel.RRKJ3', / 5 4S 1 0 2.00 0.00 2.20 2.20 0.50 4P 2 1 2.00 0.00 2.20 2.20 0.50 4P 2 1 1.00 0.00 2.20 2.20 1.50 4D 3 2 0.00 0.05 2.30 2.30 1.50 4D 3 2 0.00 0.05 2.30 2.30 2.50 ------------------------------------------------------------------------------------------------------------------------------------------------ But I can not understand why the script has two 4P rows and two 4D rows. Could you explain them for me ? Thank you. Jiming An ___________________________________________________________ ???????????? http://cn.mail.yahoo.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080522/30c24474/attachment.htm From coldwind1978 at yahoo.com.cn Thu May 22 03:36:46 2008 From: coldwind1978 at yahoo.com.cn (=?gb2312?q?=D5=EB=D2=B6=20=D6=EC?=) Date: Thu, 22 May 2008 09:36:46 +0800 (CST) Subject: [Pw_forum] ??? what's the meaning of error in compiler of sun solaris 9.0 In-Reply-To: Message-ID: <915096.69002.qm@web15803.mail.cnb.yahoo.com> Dear users: Thank you give some suggestions about compilation in solaris 9.0. The condition of my machine is as following : Sun fire 4800 and solaris sparc.I have install Sunstudio 12 in my machine. making ./configure is well done. When make pw, the errors appears. ld: fatal: Symbol referencing errors. No output written to pw.x *** Error code 1 make: Fatal error: Command failed for target `pw.x' Current working directory /zzy/espresso-4.0/PW *** Error code 1 make: Fatal error: Command failed for target `pw' Please tell me how to deal with it? Regards zhuzhenye pw_forum-request at pwscf.org ??? Send Pw_forum mailing list submissions to pw_forum at pwscf.org To subscribe or unsubscribe via the World Wide Web, visit http://www.democritos.it/mailman/listinfo/pw_forum or, via email, send a message with subject or body 'help' to pw_forum-request at pwscf.org You can reach the person managing the list at pw_forum-owner at pwscf.org When replying, please edit your Subject line so it is more specific than "Re: Contents of Pw_forum digest..." Today's Topics: 1. Re: ??? what's the meaning of error in compiler of sun (Paolo Giannozzi) 2. Re: modification of phonon programs (Paolo Giannozzi) 3. Re: electron phonon coupling / cannot remap grid on k-point list error (Paolo Giannozzi) ---------------------------------------------------------------------- Message: 1 Date: Tue, 20 May 2008 14:27:36 +0200 From: Paolo Giannozzi Subject: Re: [Pw_forum] ??? what's the meaning of error in compiler of sun To: PWSCF Forum Message-ID: <4832C3B8.6060701 at democritos.it> Content-Type: text/plain; charset=GB2312 ?? ? wrote: > Thank you give some suggestions about compilation in solaris 9.0. The > condition of my machine is as following : Sun fire 4800 and solaris > sparc.I have install Sunstudio 12 in my machine. making ./configure is > well done. When make pw, the errors appears. which errors? -- Paolo Giannozzi, Democritos and University of Udine, Italy ------------------------------ Message: 2 Date: Tue, 20 May 2008 15:24:08 +0200 From: Paolo Giannozzi Subject: Re: [Pw_forum] modification of phonon programs To: PWSCF Forum Message-ID: <4832D0F8.6030406 at democritos.it> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Eyvaz Isaev wrote: > I introduced some changes to phonon programs so that > now one can specify iq_start and iq_end keywords in > ph.in file to calculate phonons for a given set of > q-points from dyn0-file. > > If this sounds interesting I can send these modified files. it is interesting, but it is just part of the story. The phonon code presently uses only pools of processors, for k-point and plane-wave parallelization. There are however two more possible "cheap" parallelizations: over irreps, and over q-vectors. Both involve loosely coupled calculations that can be performed almost independently and thus are ideally suited for a "Grid computing" environment. Rather than via MPI calls, parallelization could be achieved by a script distributing the various calculations across many jobs, collecting the results again with a script or with an auxiliary code reading the outputd data file. This will require some changes to both the input data and the data files, but nothing dramatic. There are already two methods to supply a single q-point: the one described by Kostantin Kudin, and directly as qx, qy, qz. Both may require in the future to be modified, in order to better fit into the above picture. Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy ------------------------------ Message: 3 Date: Tue, 20 May 2008 15:28:32 +0200 From: Paolo Giannozzi Subject: Re: [Pw_forum] electron phonon coupling / cannot remap grid on k-point list error To: PWSCF Forum Message-ID: <4832D200.7070109 at democritos.it> Content-Type: text/plain; charset=ISO-8859-1; format=flowed hamad mohamed wrote: > error message > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > cannot remap grid on k-point list > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > is a peering by performing the electron phonon coupling for a > tetragonal body center unit cell, where the meshes are: > > dense 24 24 24 0 0 0 > rare 2 2 2 0 0 0 > phonon 2 2 1 > > where all the division of nk and nq that correspond to dense/rare , > dense/phonon and rare/phonon are integer. was it too much work to provide a test job? -- Paolo Giannozzi, Democritos and University of Udine, Italy ------------------------------ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum End of Pw_forum Digest, Vol 11, Issue 30 **************************************** --------------------------------- ???????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080522/573b7309/attachment.htm From akohlmey at cmm.chem.upenn.edu Thu May 22 04:03:42 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 21 May 2008 22:03:42 -0400 (EDT) Subject: [Pw_forum] ??? what's the meaning of error in compiler of sun solaris 9.0 In-Reply-To: <915096.69002.qm@web15803.mail.cnb.yahoo.com> References: <915096.69002.qm@web15803.mail.cnb.yahoo.com> Message-ID: On Thu, 22 May 2008, ???? ?? wrote: XX> Dear users: XX> Thank you give some suggestions about compilation in solaris 9.0. XX> The condition of my machine is as following : Sun fire 4800 and solaris XX> sparc.I have install Sunstudio 12 in my machine. making ./configure XX> is well done. When make pw, the errors appears. XX> ld: fatal: Symbol referencing errors. No output written to pw.x XX> *** Error code 1 XX> make: Fatal error: Command failed for target `pw.x' XX> Current working directory /zzy/espresso-4.0/PW XX> *** Error code 1 XX> make: Fatal error: Command failed for target `pw' XX> Please tell me how to deal with it? how about? rm -rf /zzy/* that would at least save us from having the see the same mail over and over again... axel. XX> XX> Regards XX> XX> zhuzhenye XX> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From hande at newton.physics.metu.edu.tr Thu May 22 07:48:49 2008 From: hande at newton.physics.metu.edu.tr (Hande Ustunel) Date: Thu, 22 May 2008 08:48:49 +0300 (EEST) Subject: [Pw_forum] Why does the script of example As has two 4P rows and two 4Drows. In-Reply-To: <833102.6034.qm@web15002.mail.cnb.yahoo.com> Message-ID: > But I can not understand why the script has two 4P rows and two 4D rows. > Could you explain them for me ? Thank you. rel=2 means that the pseudopotential includes spin-orbit coupling. Thus each of the repeated lines correspond to a spin-orbit split state as is designated by the final column. For more information, I recommend that you take a look at the txt file INPUT_LD1 included in the atomic folder inside the espresso package, especially under section 1.1). Best wishes, Hande -- Hande Ustunel Department of Physics Office 439 Middle East Technical University Ankara 06531, Turkey Tel : +90 312 210 3264 http://www.physics.metu.edu.tr/~hande From lawrence_lee_lee at yahoo.com.hk Thu May 22 08:20:37 2008 From: lawrence_lee_lee at yahoo.com.hk (Lawrence Lee) Date: Thu, 22 May 2008 14:20:37 +0800 Subject: [Pw_forum] Stress tensor from pw.x and cp.x Message-ID: <1211437237.6454.15.camel@scg11> Dear all, Since my calculation is really simple, I am not going to attach my input file here. I use the QE-3.1.1 code, and perform scf calculation using pw.x on a 64-atom cell, which has a perfect fcc structure, using only the gamma point. I obtain a stress tensor then. Later on I use exactly the same structure and cell and cut-off's, but using cp.x to perform a damped dynamics on the electrons, keeping the atoms fixed. I also obtain a stress tensor. However, the results between pw.x and cp.x is different, apart from the difference in units. The cp.x results are generally about 5~10 GPa above that of pw.x. I find this quite confusing. Is the method of calculation of stress tensor by these two programmes different? Thank you very much for solving my doubt. -- S.H. Lee M.Phil Physics Division The CUHK Graduate School _______________________________________ ?x?????? - Yahoo! Messenger ???????]?????W?????????????????????????o???????????W?r???????????????????f???????????? http://messenger.yahoo.com.hk From marzari at MIT.EDU Thu May 22 08:36:09 2008 From: marzari at MIT.EDU (Nicola Marzari) Date: Thu, 22 May 2008 02:36:09 -0400 Subject: [Pw_forum] Stress tensor from pw.x and cp.x In-Reply-To: <1211437237.6454.15.camel@scg11> References: <1211437237.6454.15.camel@scg11> Message-ID: <48351459.60002@mit.edu> Dear Lawrence, the only suggestions that comes to mind is this - the stress tensors converges to its "true" values more slowly with energy cutoff then other quantities. Usually the error at standard cutoffs is fairly "rigid", i.e. due to contributions that are not sensitive to the chemical environment, and so you can even correct for that empirically. CP and PWscf have a different way of treating augmentation charges, so that's the only major difference that comes to mind - but it would apply to ultrasoft pseudo (that's why posting your input would have helped). Bottom line - let's use QE-4.0 (i.e. download it now) and retest with increasing cutoff, and if you are using ultrasoft pseudopotentials, throw in for good measure a high charge density cutoff (10-12 times the wavefunctions). In CP, test also for the box grid size (nr1b...), increasing values. And then maybe post again, at least the results and an input file. Of course, if it is ultrasoft, and your nr1b is not really that good, that could explain it right away. nicola Lawrence Lee wrote: > Dear all, > > Since my calculation is really simple, I am not going to attach my input > file here. I use the QE-3.1.1 code, and perform scf calculation using > pw.x on a 64-atom cell, which has a perfect fcc structure, using only > the gamma point. I obtain a stress tensor then. > > Later on I use exactly the same structure and cell and cut-off's, but > using cp.x to perform a damped dynamics on the electrons, keeping the > atoms fixed. I also obtain a stress tensor. > > However, the results between pw.x and cp.x is different, apart from the > difference in units. The cp.x results are generally about 5~10 GPa above > that of pw.x. > > I find this quite confusing. Is the method of calculation of stress > tensor by these two programmes different? > > Thank you very much for solving my doubt. -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From giannozz at democritos.it Thu May 22 08:41:14 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 22 May 2008 08:41:14 +0200 Subject: [Pw_forum] ??? what's the meaning of error in compiler of sun solaris 9.0 In-Reply-To: <915096.69002.qm@web15803.mail.cnb.yahoo.com> References: <915096.69002.qm@web15803.mail.cnb.yahoo.com> Message-ID: <4835158A.7080207@democritos.it> ?? ? wrote: > ld: fatal: Symbol referencing errors. No output written to pw.x this is not the error. There are other errors appearing before this one. It is the first error message that is significant, not the last -- Paolo Giannozzi, Democritos and University of Udine, Italy From lawrence_lee_lee at yahoo.com.hk Thu May 22 08:58:57 2008 From: lawrence_lee_lee at yahoo.com.hk (Lawrence Lee) Date: Thu, 22 May 2008 14:58:57 +0800 Subject: [Pw_forum] Stress tensor from pw.x and cp.x In-Reply-To: <48351459.60002@mit.edu> References: <1211437237.6454.15.camel@scg11> <48351459.60002@mit.edu> Message-ID: <1211439537.16747.3.camel@scg11> Dear Nicola, Thank you very much for giving me some ideas about the issue! Indeed, I am using ultrasoft pseudopotentials. And therefore, I've set the nrb's carefully using the formula, "nr1b=2*rcut*nr1/Lx", and make it a bit larger than values calculated with this equation. However, you remind me that I may not have a high enough ecutrho. My ecutwfc is 35 Ryd and 150 for ecutrho. This might not be enough... I will try a higher value on ecutrho to see if there are any difference. If there is still the problem, I will then have to try the QE-4 package. Thank you very much! -- S.H. Lee M.Phil Physics Division The CUHK Graduate School On Thu, 2008-05-22 at 02:36 -0400, Nicola Marzari wrote: > > Dear Lawrence, > > > the only suggestions that comes to mind is this - the stress tensors > converges to its "true" values more slowly with energy cutoff then > other quantities. Usually the error at standard cutoffs is > fairly "rigid", i.e. due to contributions that are not sensitive to > the chemical environment, and so you can even correct for that > empirically. > > CP and PWscf have a different way of treating augmentation charges, > so that's the only major difference that comes to mind - but it would > apply to ultrasoft pseudo (that's why posting your input would have helped). > > Bottom line - let's use QE-4.0 (i.e. download it now) and retest > with increasing cutoff, and if you are using ultrasoft pseudopotentials, > throw in for good measure a high charge density cutoff (10-12 times the > wavefunctions). In CP, test also for the box grid size (nr1b...), > increasing values. And then maybe post again, at least the results > and an input file. Of course, if it is ultrasoft, and your nr1b is not > really that good, that could explain it right away. > > > nicola > > > > Lawrence Lee wrote: > > Dear all, > > > > Since my calculation is really simple, I am not going to attach my input > > file here. I use the QE-3.1.1 code, and perform scf calculation using > > pw.x on a 64-atom cell, which has a perfect fcc structure, using only > > the gamma point. I obtain a stress tensor then. > > > > Later on I use exactly the same structure and cell and cut-off's, but > > using cp.x to perform a damped dynamics on the electrons, keeping the > > atoms fixed. I also obtain a stress tensor. > > > > However, the results between pw.x and cp.x is different, apart from the > > difference in units. The cp.x results are generally about 5~10 GPa above > > that of pw.x. > > > > I find this quite confusing. Is the method of calculation of stress > > tensor by these two programmes different? > > > > Thank you very much for solving my doubt. _______________________________________ ?x?????? - Yahoo! Messenger ???????]?????W?????????????????????????o???????????W?r???????????????????f???????????? http://messenger.yahoo.com.hk From igerber at insa-toulouse.fr Thu May 22 08:52:57 2008 From: igerber at insa-toulouse.fr (Iann Gerber) Date: Thu, 22 May 2008 08:52:57 +0200 Subject: [Pw_forum] NC PP generation for GIPAW calc Message-ID: <48351849.9080901@insa-toulouse.fr> Dear pw_scf users, My question is quite simple: How one can generate new NC-PPs containing GIPAW datas similar to the ones used in the example folder in the 4.0 version of PW_SCF? I found the lgipaw_reconstruction tag in the PP module but the created UPF file doesn't have similar headers and basically it can't be used with the gipaw.x available in the 4.0 release... What is the correct recipe ? Thanks in advance for the provided help... -- Iann Gerber LPCNO INSA - Toulouse email: igerber at insa-toulouse.fr 135, Avenue de Rangueil Tel: +33 5 61 55 96 64 31077 CEDEX 04 Toulouse Fax: +33 5 61 55 96 97 France From sks.jnc at gmail.com Thu May 22 10:40:25 2008 From: sks.jnc at gmail.com (S. K. S.) Date: Thu, 22 May 2008 14:10:25 +0530 Subject: [Pw_forum] XCRYSDEN Message-ID: Dear PWscf Users, Is there any option in XCRYSDEN software where we can increase the size or the font of the "Coordinate System" logo which usually comes below in the left side corner of any XCRYSDEN Picture????? regards, S. K. S. JNCASR Bangalore -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080522/5a5411ed/attachment.htm From fnog at teor.fis.uc.pt Thu May 22 10:31:47 2008 From: fnog at teor.fis.uc.pt (Fernando Nogueira) Date: Thu, 22 May 2008 09:31:47 +0100 Subject: [Pw_forum] Relativistic semi-core potentials Message-ID: <901149B7-9F65-45CF-8A94-E527106C12FC@teor.fis.uc.pt> Dear pwscf users, I have been trying to generate a relativistic ultrasoft potential for Cr that includes semi-core electrons. So far I had no sucess: I keep getting the same error message about a discrepancy in the number of pseudo and all-electron electrons. Am I doing something wrong? Is this combination available through the atomic code? Thanks! Fernando Fernando Nogueira Centre for Computational Physics and Physics Department University of Coimbra Rua Larga 3004-516 COIMBRA PORTUGAL Phone: + 351 239410114 Fax: + 351 239829158 email: fnog at teor.fis.uc.pt URL: http://nautilus.fis.uc.pt/~fnog/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080522/d0882e81/attachment.htm From degironc at sissa.it Thu May 22 13:22:01 2008 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 22 May 2008 13:22:01 +0200 Subject: [Pw_forum] Relativistic semi-core potentials In-Reply-To: <901149B7-9F65-45CF-8A94-E527106C12FC@teor.fis.uc.pt> References: <901149B7-9F65-45CF-8A94-E527106C12FC@teor.fis.uc.pt> Message-ID: <48355759.5000307@sissa.it> Fernando Nogueira wrote: > Dear pwscf users, > > I have been trying to generate a relativistic ultrasoft potential for > Cr that includes semi-core electrons. So far I had no sucess: I keep > getting the same error message about a discrepancy in the number of > pseudo and all-electron electrons. Am I doing something wrong? Is this > combination available through the atomic code? without seeing your input is quite difficult to have any ideas about your problem... stefano > Thanks! > > Fernando > > > Fernando Nogueira > Centre for Computational Physics and > Physics Department > University of Coimbra > Rua Larga > 3004-516 COIMBRA > PORTUGAL > > Phone: + 351 239410114 > Fax: + 351 239829158 > email: fnog at teor.fis.uc.pt > URL: http://nautilus.fis.uc.pt/~fnog/ > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From fnog at teor.fis.uc.pt Thu May 22 13:28:06 2008 From: fnog at teor.fis.uc.pt (Fernando Nogueira) Date: Thu, 22 May 2008 12:28:06 +0100 Subject: [Pw_forum] Relativistic semi-core potentials In-Reply-To: <48355759.5000307@sissa.it> References: <901149B7-9F65-45CF-8A94-E527106C12FC@teor.fis.uc.pt> <48355759.5000307@sissa.it> Message-ID: Dear Stefano, Sorry, I forgot to add it. My input is: *************** &input title='Cr', zed=24., rel=2, config='[Ar] 3d5.0 4s1.0 4p0', dft='PBE', iswitch=3 / &inputp lloc=0, pseudotype=3, file_pseudopw='Cr.UPF', nlcc=.false., author='FNOG', / 10 3P 2 1 2.00 0.00 1.60 2.40 0.5 3P 2 1 4.00 0.00 1.60 2.40 1.5 4S 2 0 1.00 0.00 1.60 2.40 0.5 4P 3 1 0.00 0.00 1.60 2.40 0.5 4P 3 1 0.00 0.00 1.60 2.40 1.5 3D 3 2 3.00 0.00 1.60 2.40 1.5 3D 3 2 0.00 -0.20 1.60 2.40 1.5 3D 3 2 2.00 0.00 1.60 2.40 2.5 3D 3 2 0.00 -0.20 1.60 2.40 2.5 3S 1 0 2.00 0.00 1.60 2.40 0.5 ************************** Thanks, Fernando On May 22, 2008, at 12:22, Stefano de Gironcoli wrote: > Fernando Nogueira wrote: >> Dear pwscf users, >> >> I have been trying to generate a relativistic ultrasoft potential for >> Cr that includes semi-core electrons. So far I had no sucess: I keep >> getting the same error message about a discrepancy in the number of >> pseudo and all-electron electrons. Am I doing something wrong? Is >> this >> combination available through the atomic code? > without seeing your input is quite difficult to have any ideas about > your problem... > stefano > >> Thanks! >> >> Fernando >> >> >> Fernando Nogueira >> Centre for Computational Physics and >> Physics Department >> University of Coimbra >> Rua Larga >> 3004-516 COIMBRA >> PORTUGAL >> >> Phone: + 351 239410114 >> Fax: + 351 239829158 >> email: fnog at teor.fis.uc.pt >> URL: http://nautilus.fis.uc.pt/~fnog/ > > >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 > Fernando Nogueira Centre for Computational Physics and Physics Department University of Coimbra Rua Larga 3004-516 COIMBRA PORTUGAL Phone: + 351 239410114 Fax: + 351 239829158 email: fnog at teor.fis.uc.pt URL: http://nautilus.fis.uc.pt/~fnog/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080522/9dd6afef/attachment-0001.htm From dalcorso at sissa.it Thu May 22 13:47:18 2008 From: dalcorso at sissa.it (Dal Corso Andrea) Date: Thu, 22 May 2008 13:47:18 +0200 Subject: [Pw_forum] Relativistic semi-core potentials In-Reply-To: References: <901149B7-9F65-45CF-8A94-E527106C12FC@teor.fis.uc.pt> <48355759.5000307@sissa.it> Message-ID: <1211456838.3379.21.camel@dhpc-5-03.sissa.it> On Thu, 2008-05-22 at 12:28 +0100, Fernando Nogueira wrote: > Dear Stefano, > > > Sorry, I forgot to add it. My input is: > > > *************** > &input > title='Cr', > zed=24., > rel=2, > config='[Ar] 3d5.0 4s1.0 4p0', To make a pseudo as you are trying to do you should specify here config='[Ar] 3d3 3d2 4s1 4p0' otherwise the ld1 code distributes the electrons as 3d4 3d1 and then it finds a mismatch with the pseudo configuration. Hope this helps, Andrea > dft='PBE', > iswitch=3 > / > &inputp > lloc=0, > pseudotype=3, > file_pseudopw='Cr.UPF', > nlcc=.false., > author='FNOG', > / > 10 > 3P 2 1 2.00 0.00 1.60 2.40 0.5 > 3P 2 1 4.00 0.00 1.60 2.40 1.5 > 4S 2 0 1.00 0.00 1.60 2.40 0.5 > 4P 3 1 0.00 0.00 1.60 2.40 0.5 > 4P 3 1 0.00 0.00 1.60 2.40 1.5 > 3D 3 2 3.00 0.00 1.60 2.40 1.5 > 3D 3 2 0.00 -0.20 1.60 2.40 1.5 > 3D 3 2 2.00 0.00 1.60 2.40 2.5 > 3D 3 2 0.00 -0.20 1.60 2.40 2.5 > 3S 1 0 2.00 0.00 1.60 2.40 0.5 > ************************** > > > Thanks, > > > Fernando > > On May 22, 2008, at 12:22, Stefano de Gironcoli wrote: > > > Fernando Nogueira wrote: > > > Dear pwscf users, > > > > > > I have been trying to generate a relativistic ultrasoft potential > > > for > > > Cr that includes semi-core electrons. So far I had no sucess: I > > > keep > > > getting the same error message about a discrepancy in the number > > > of > > > pseudo and all-electron electrons. Am I doing something wrong? Is > > > this > > > combination available through the atomic code? > > without seeing your input is quite difficult to have any ideas > > about > > your problem... > > stefano > > > > > Thanks! > > > > > > Fernando > > > > > > > > > Fernando Nogueira > > > Centre for Computational Physics and > > > Physics Department > > > University of Coimbra > > > Rua Larga > > > 3004-516 COIMBRA > > > PORTUGAL > > > > > > Phone: + 351 239410114 > > > Fax: + 351 239829158 > > > email: fnog at teor.fis.uc.pt > > > URL: http://nautilus.fis.uc.pt/~fnog/ > > 7Efnog/> > > > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > 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 > > > > Fernando Nogueira > Centre for Computational Physics and > Physics Department > University of Coimbra > Rua Larga > 3004-516 COIMBRA > PORTUGAL > > > Phone: + 351 239410114 > Fax: + 351 239829158 > email: fnog at teor.fis.uc.pt > URL: http://nautilus.fis.uc.pt/~fnog/ > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Andrea Dal Corso Tel. 0039-040-3787428 SISSA, Via Beirut 2/4 Fax. 0039-040-3787528 34014 Trieste (Italy) e-mail: dalcorso at sissa.it From dalcorso at sissa.it Thu May 22 15:36:34 2008 From: dalcorso at sissa.it (Dal Corso Andrea) Date: Thu, 22 May 2008 15:36:34 +0200 Subject: [Pw_forum] Relativistic semi-core potentials In-Reply-To: References: <901149B7-9F65-45CF-8A94-E527106C12FC@teor.fis.uc.pt> <48355759.5000307@sissa.it> Message-ID: <1211463394.3379.46.camel@dhpc-5-03.sissa.it> On Thu, 2008-05-22 at 12:28 +0100, Fernando Nogueira wrote: > Dear Stefano, > > > Sorry, I forgot to add it. My input is: > > > *************** > &input > title='Cr', > zed=24., > rel=2, > config='[Ar] 3d5.0 4s1.0 4p0', > dft='PBE', > iswitch=3 > / > &inputp > lloc=0, > pseudotype=3, > file_pseudopw='Cr.UPF', > nlcc=.false., > author='FNOG', > / > 10 > 3P 2 1 2.00 0.00 1.60 2.40 0.5 > 3P 2 1 4.00 0.00 1.60 2.40 1.5 > 4S 2 0 1.00 0.00 1.60 2.40 0.5 > 4P 3 1 0.00 0.00 1.60 2.40 0.5 > 4P 3 1 0.00 0.00 1.60 2.40 1.5 > 3D 3 2 3.00 0.00 1.60 2.40 1.5 > 3D 3 2 0.00 -0.20 1.60 2.40 1.5 > 3D 3 2 2.00 0.00 1.60 2.40 2.5 > 3D 3 2 0.00 -0.20 1.60 2.40 2.5 > 3S 1 0 2.00 0.00 1.60 2.40 0.5 A few comments: The local potential cannot be US so the two radii must be the same. Then if you want to have a 4s with nonlocal projectors you need at least two energies for the 4s or you have to request a NC 4s channel setting two equal radii. With these large NC core radii the RRKJ has problems to find q_i for the semicore states so I suspect it will be quite difficult to obtain a PP with these radii but I have not extensive experience with PP with semicore states. You can also experiment with the option tm=.true. To make a pseudo with semicore states is still quite difficult with ld1. In general to make a fully relativistic PP is not so difficult if you have a good scalar relavistic PP. So I would start from the SR pseudo. Hope this helps, although the problem of making good PPs with semicore states with ld1 is not totally solved. Andrea > > Thanks, > > > Fernando > > On May 22, 2008, at 12:22, Stefano de Gironcoli wrote: > > > Fernando Nogueira wrote: > > > Dear pwscf users, > > > > > > I have been trying to generate a relativistic ultrasoft potential > > > for > > > Cr that includes semi-core electrons. So far I had no sucess: I > > > keep > > > getting the same error message about a discrepancy in the number > > > of > > > pseudo and all-electron electrons. Am I doing something wrong? Is > > > this > > > combination available through the atomic code? > > without seeing your input is quite difficult to have any ideas > > about > > your problem... > > stefano > > > > > Thanks! > > > > > > Fernando > > > > > > > > > Fernando Nogueira > > > Centre for Computational Physics and > > > Physics Department > > > University of Coimbra > > > Rua Larga > > > 3004-516 COIMBRA > > > PORTUGAL > > > > > > Phone: + 351 239410114 > > > Fax: + 351 239829158 > > > email: fnog at teor.fis.uc.pt > > > URL: http://nautilus.fis.uc.pt/~fnog/ > > 7Efnog/> > > > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > 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 > > > > Fernando Nogueira > Centre for Computational Physics and > Physics Department > University of Coimbra > Rua Larga > 3004-516 COIMBRA > PORTUGAL > > > Phone: + 351 239410114 > Fax: + 351 239829158 > email: fnog at teor.fis.uc.pt > URL: http://nautilus.fis.uc.pt/~fnog/ > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Andrea Dal Corso Tel. 0039-040-3787428 SISSA, Via Beirut 2/4 Fax. 0039-040-3787528 34014 Trieste (Italy) e-mail: dalcorso at sissa.it From ramirocardona at gmail.com Thu May 22 16:01:19 2008 From: ramirocardona at gmail.com (Ramiro Cardona) Date: Thu, 22 May 2008 09:01:19 -0500 Subject: [Pw_forum] Error in cppp.x Message-ID: Dear all I'm trying to run the tutorial examples h2o_mol1.in and h2o_mol.cppp-dens.in in page: http://people.sissa.it/~degironc/QE-Tutorial/tutorial_cp.htm cp.x < h2o.mol1.in runs OK but cppp.x < h2o_mol.cppp-dens.in shows the following error: # FROM IOTK LIBRARY, VERSION 1.1.0development # UNRECOVERABLE ERROR (ierr=-1) # ERROR IN: iotk_scan_dat (iotk_dat.spp:768) # CVS Revision: 1.5 # Dat not found name=ATOM_TYPE I'm using espresso 4.0 and gfortran compiler. But wit ifort we have the same error With espresso-3.2.3 both commands run OK (no errors) Best regards Ramiro Cardona Physics Departament Universidad Nacional de Colombia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080522/a74e4337/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: h2o_mol1.in Type: application/octet-stream Size: 990 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20080522/a74e4337/attachment.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: h2o_mol.cppp-dens.in Type: application/octet-stream Size: 170 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20080522/a74e4337/attachment-0001.obj From chenhanghuipwscf at gmail.com Fri May 23 00:02:19 2008 From: chenhanghuipwscf at gmail.com (alan chen) Date: Thu, 22 May 2008 18:02:19 -0400 Subject: [Pw_forum] charge density Message-ID: <22ae3ca40805221502y48522711t42797d1c36d9795f@mail.gmail.com> Dear PWSCF users, I want to know how the charge density is normalized in PWSCF. For example, I have calculated bulk STO. The integral of charge density over the unit cell is 0.162. I normalize it to the total number of electron which is 40. Then I calculate bulk LAO in the unit cell of the same size, same k-point sample and same energy cutoff. The integral of charge density over the unit cell is 0.19. The total number of electrons is 32 for LAO. So how does PWSCF normalize charge density for different cases? Thank you. Hanghui Department of Physics, Yale University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080522/ddb0662b/attachment.htm From akohlmey at cmm.chem.upenn.edu Thu May 22 23:36:12 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Thu, 22 May 2008 17:36:12 -0400 (EDT) Subject: [Pw_forum] charge density In-Reply-To: <22ae3ca40805221502y48522711t42797d1c36d9795f@mail.gmail.com> References: <22ae3ca40805221502y48522711t42797d1c36d9795f@mail.gmail.com> Message-ID: On Thu, 22 May 2008, alan chen wrote: AC> Dear PWSCF users, AC> I want to know how the charge density is normalized in PWSCF. the sum over all gridpoints should give the number of electrons. the code actually uses this property to check whether real and g-space are consistent. AC> For example, I have calculated bulk STO. The integral of charge AC> density over the unit cell is 0.162. I normalize it to the total number of AC> electron which is 40. how do you do the integral? axel. AC> Then I calculate bulk LAO in the unit cell of the same size, same AC> k-point sample and same energy cutoff. The integral of charge density over AC> the unit cell is 0.19. The total number of electrons is 32 for LAO. AC> So how does PWSCF normalize charge density for different cases? AC> Thank you. AC> AC> Hanghui AC> Department of Physics, AC> Yale University AC> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From padmaja_patnaik at yahoo.co.uk Fri May 23 06:20:35 2008 From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik) Date: Fri, 23 May 2008 04:20:35 +0000 (GMT) Subject: [Pw_forum] Problem in compilation Message-ID: <207921.73722.qm@web25406.mail.ukl.yahoo.com> An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080523/06d9c653/attachment.htm From rprasad at iitk.ac.in Fri May 23 07:25:06 2008 From: rprasad at iitk.ac.in (rprasad at iitk.ac.in) Date: Fri, 23 May 2008 10:55:06 +0530 (IST) Subject: [Pw_forum] Phonon DOS in noncubic materials In-Reply-To: <207921.73722.qm@web25406.mail.ukl.yahoo.com> References: <207921.73722.qm@web25406.mail.ukl.yahoo.com> Message-ID: <1604.172.28.5.210.1211520306.squirrel@newwebmail.iitk.ac.in> Dear PWSCF users and developer, There is a comment in matdyn.f90 that it may not work for noncubic materials for calculating phonon DOS. Why is so? Is there a simple way to modify the program for noncubic materials? R. Prasad IIT Kanpur From giannozz at democritos.it Fri May 23 09:05:42 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 23 May 2008 09:05:42 +0200 Subject: [Pw_forum] charge density In-Reply-To: <22ae3ca40805221502y48522711t42797d1c36d9795f@mail.gmail.com> References: <22ae3ca40805221502y48522711t42797d1c36d9795f@mail.gmail.com> Message-ID: <48366CC6.5060603@democritos.it> alan chen wrote: > I want to know how the charge density is normalized in PWSCF. it is not "normalized": it has the value it should have. Just notice that it does NOT include the charge -e: the "true" charge density is -e*rho > For example, I have calculated bulk STO. The integral of charge > density over the unit cell is 0.162. I normalize it to the total number > of electron which is 40. the (correct) integral of the charge density over the unit cell is 40. In real space, the integral is (sum over grid points)*(volume element). The volume element is the volume of the cell (omega) divided by the number of grid points (nr1*nr2*nr3). In G-space, the integral is simply omega*rho(G=0). P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From baroni at sissa.it Fri May 23 09:26:21 2008 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 23 May 2008 09:26:21 +0200 Subject: [Pw_forum] Phonon DOS in noncubic materials In-Reply-To: <1604.172.28.5.210.1211520306.squirrel@newwebmail.iitk.ac.in> References: <207921.73722.qm@web25406.mail.ukl.yahoo.com> <1604.172.28.5.210.1211520306.squirrel@newwebmail.iitk.ac.in> Message-ID: I think (others may want to confirm or deny) that this depends of the non-analytic behavior of the dynamical matrix in the long-wavelength limit. Because of this, phonon frequencies at q=0 are strictly speaking not defined. Their limit as q->0 is indeed well defined only once the direction of q and of the phonon polarization is specified. For cubic materials, this non-analiticity gives rise to the well known LO-TO splitting, whereas for crystals of lower symmetry the situation is more complicated. If the DOS is calculated using a very fine mesh of q points, I would expect that the result would be independent on what happens around q=0. If, instead, too few points are used, I would not be surprised if the above-mentioned non-analytic behavior would severly undermine the accuracy of any sensible interpolation procedure needed for any integration (such as the one used for DOS calculations). Hope this is not too wrong, and of some help as well. SB On May 23, 2008, at 7:25 AM, rprasad at iitk.ac.in wrote: > Dear PWSCF users and developer, > > There is a comment in matdyn.f90 that it may not work for noncubic > materials for calculating phonon DOS. Why is so? Is there a simple > way to > modify the program for noncubic materials? > > R. Prasad > IIT Kanpur > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080523/008d7d52/attachment.htm From giannozz at democritos.it Fri May 23 09:31:07 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 23 May 2008 09:31:07 +0200 Subject: [Pw_forum] Problem in compilation In-Reply-To: <207921.73722.qm@web25406.mail.ukl.yahoo.com> References: <207921.73722.qm@web25406.mail.ukl.yahoo.com> Message-ID: <483672BB.90404@democritos.it> Padmaja Patnaik wrote: > Please suggest. 1) use the new version 2) read and understand error messages. If your computer says: "ar: iotk_attr+CHARACTER1_0.o: No such file or directory" this means that iotk_attr+CHARACTER1_0.o is not there, and it is not there because iotk_attr+CHARACTER1_0.f90 was not compiled. Why wasn't it compiled? -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Fri May 23 09:39:44 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 23 May 2008 09:39:44 +0200 Subject: [Pw_forum] Phonon DOS in noncubic materials In-Reply-To: References: <207921.73722.qm@web25406.mail.ukl.yahoo.com> <1604.172.28.5.210.1211520306.squirrel@newwebmail.iitk.ac.in> Message-ID: <483674C0.6020109@democritos.it> Stefano Baroni wrote: > I think (others may want to confirm or deny) that this depends of the > non-analytic behavior of the dynamical matrix in the long-wavelength > limit. Because of this, phonon frequencies at q=0 are strictly speaking > not defined. Their limit as q->0 is indeed well defined only once the > direction of q and of the phonon polarization is specified. For cubic > materials, this non-analiticity gives rise to the well known LO-TO > splitting, whereas for crystals of lower symmetry the situation is more > complicated. If the DOS is calculated using a very fine mesh of q > points, I would expect that the result would be independent on what > happens around q=0. If, instead, too few points are used, I would not be > surprised if the above-mentioned non-analytic behavior would severly > undermine the accuracy of any sensible interpolation procedure needed > for any integration (such as the one used for DOS calculations). Hope > this is not too wrong, and of some help as well. SB confirmed. I wrote some time ago the warning about phonon dos in noncubic materials, because it wasn't clear to me what to do at q=0 in that case. I don't expect a large error, since this is a problem at just a single q-point, but it is safer to advertise it. Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Fri May 23 09:49:06 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 23 May 2008 09:49:06 +0200 Subject: [Pw_forum] Error in cppp.x In-Reply-To: References: Message-ID: <483676F2.8070000@democritos.it> Ramiro Cardona wrote: > cppp.x < h2o_mol.cppp-dens.in > shows the following error: [...] I'm using espresso 4.0 and > gfortran compiler. But with ifort we have the same error > > With espresso-3.2.3 both commands run OK (no errors) thank you for your (clear and detailed) bug report. I am afraid that when the file format was slightly changed, the CP postprocessing code was forgotten. It will be fixed soon Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From rprasad at iitk.ac.in Fri May 23 12:38:32 2008 From: rprasad at iitk.ac.in (Rajendra Prasad fc phy) Date: Fri, 23 May 2008 16:08:32 +0530 (IST) Subject: [Pw_forum] Phonon DOS in noncubic materials In-Reply-To: References: <207921.73722.qm@web25406.mail.ukl.yahoo.com> <1604.172.28.5.210.1211520306.squirrel@newwebmail.iitk.ac.in> Message-ID: Dear Profs. Baroni and Giannozzi, Thank you for your prompt response and the clarification. R. Prasad IIT Kanpur On Fri, 23 May 2008, Stefano Baroni wrote: > I think (others may want to confirm or deny) that this depends of the > non-analytic behavior of the dynamical matrix in the long-wavelength > limit. Because of this, phonon frequencies at q=0 are strictly > speaking not defined. Their limit as q->0 is indeed well defined only > once the direction of q and of the phonon polarization is specified. > For cubic materials, this non-analiticity gives rise to the well known > LO-TO splitting, whereas for crystals of lower symmetry the situation > is more complicated. If the DOS is calculated using a very fine mesh > of q points, I would expect that the result would be independent on > what happens around q=0. If, instead, too few points are used, I would > not be surprised if the above-mentioned non-analytic behavior would > severly undermine the accuracy of any sensible interpolation procedure > needed for any integration (such as the one used for DOS > calculations). Hope this is not too wrong, and of some help as well. SB > > On May 23, 2008, at 7:25 AM, rprasad at iitk.ac.in wrote: > > > Dear PWSCF users and developer, > > > > There is a comment in matdyn.f90 that it may not work for noncubic > > materials for calculating phonon DOS. Why is so? Is there a simple > > way to > > modify the program for noncubic materials? > > > > R. Prasad > > IIT Kanpur > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - > Trieste > [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une morale > de la pens?e - Jean Piaget > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > From eariel99 at gmail.com Fri May 23 18:33:53 2008 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Fri, 23 May 2008 12:33:53 -0400 Subject: [Pw_forum] problem changing the time step with pwscf Message-ID: Hi, I noticed that running molecular dynamic calculations , the time step (dt) cannot be changed if one restarts from a previous run (restart_mode='restart'). This happens at least in versions 4.0 and 3.2. If it is done, pw.x runs without complain (see note below), but the velocities and the kinetic energies are not correctly calculated. Also, in the prefix.msd.dat file, the times are calculated as dt*istep, producing a jump in time if dt is changed. The time should be something like previous_final_time+(istep-previous_nstep)*dt. Note that the time is correctly reported in the standard output. This can be tested with example04, running it mannually to avoid deletion of the temporary save, and restarting wiht a modified input file si.md8.in using restart_mode='restart', dt=10, nstep=150, Note: There is also a warning message when restarting in example 4: RECOVER from restart file failed: file not found. Here is my bash script (just one more) to extract the temperature and the energies from the output file. The jumps are seen plotting the dat files. INFILE=si.md8.out SUFFIX=si8.dat grep kbar $INFILE |awk '{print $6}' >>p_${SUFFIX} grep 'temperature =' $INFILE |awk '{print $3}' >>t_${SUFFIX} grep 'Ekin + Etot (const)' $INFILE |awk '{print $6}' >>etotal_${SUFFIX} grep 'kinetic energy (Ekin) =' $INFILE |awk '{print $5}' >>ekin_${SUFFIX} paste etotal_${SUFFIX} ekin_${SUFFIX}|awk '{printf("%7.7f \n", $1-$2)}' >epot_${SUFFIX} Why change the time step? Maybe just to check the stability of the simulations. Or maybe a large dt is enough for driving the system to a certain temperature near equilibrium, but a smaller one is need after the thermostat is switched off. -- Eduardo Menendez -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080523/1334e33c/attachment-0001.htm From chen_shao_hua197 at yahoo.com.tw Fri May 23 18:56:30 2008 From: chen_shao_hua197 at yahoo.com.tw (=?big5?q?=B3=AF=20=A4=D6=B5=D8?=) Date: Sat, 24 May 2008 00:56:30 +0800 (CST) Subject: [Pw_forum] About nelec and tot_charge again In-Reply-To: <483148AC.9010402@nest.sns.it> Message-ID: <309818.40248.qm@web73013.mail.tp2.yahoo.com> Dear Paolo, I wondering what is meaning that you said "in the limits of the RBA" ? For example, if I want shift the Fermi level of diamond downward to valence band.(make it as p-type doped diamond) x% doping , set nelec=8-(2*x%) . what is limit of x ? Is 10% , 1% setting OK ? Thanks in advance max --- Paolo Giannozzi ?? > ? ?? wrote: > > > I heard there is a method call "Rigid Band > > Approximation"(RBA). In order to shift Fermi level > to > > conduction band or valence band in semiconductor, > does > > it make sense just set "nelec" parameter only ? > > it does (in the limits of the RBA, of course) > > Paolo > -- > Paolo Giannozzi, Democritos and University of Udine, > Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ____________________________________________________________________________________________ 2G??????Yahoo??????2.0??????????? http://tw.mg0.mail.yahoo.com/dc/landing From giannozz at democritos.it Fri May 23 19:08:31 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 23 May 2008 19:08:31 +0200 Subject: [Pw_forum] About nelec and tot_charge again In-Reply-To: <309818.40248.qm@web73013.mail.tp2.yahoo.com> References: <309818.40248.qm@web73013.mail.tp2.yahoo.com> Message-ID: <428DD657-71FB-41DD-99A4-7B3DC223C6AD@democritos.it> On May 23, 2008, at 18:56 , ? ?? wrote: > I wondering what is meaning that you said "in the > limits of the RBA" ? the A of RBA stands for "Approximation". What are the limits of an approximation? sometimes it doesn't approximate well. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From kazempoor2000 at yahoo.com Sat May 24 08:16:20 2008 From: kazempoor2000 at yahoo.com (ali kazempoor) Date: Fri, 23 May 2008 23:16:20 -0700 (PDT) Subject: [Pw_forum] relaxation Message-ID: <577932.94022.qm@web33108.mail.mud.yahoo.com> Dear All for relaxation a surface, i want to fix positions of one layer . could you help me how can i do that? From degironc at sissa.it Sat May 24 10:57:40 2008 From: degironc at sissa.it (Stefano de Gironcoli) Date: Sat, 24 May 2008 10:57:40 +0200 Subject: [Pw_forum] relaxation In-Reply-To: <577932.94022.qm@web33108.mail.mud.yahoo.com> References: <577932.94022.qm@web33108.mail.mud.yahoo.com> Message-ID: <4837D884.4030005@sissa.it> Dear Ali, a good start would be to read the documentation about atomic positions... especially the use of if_pos variables. hope it helps. stefano de Gironcoli -- SISSA and DEMOCRITOS PS: don't forget to include your affiliation in your massages. ali kazempoor wrote: > Dear All > for relaxation a surface, i want to fix positions of > one layer . could you help me how can i do that? > From giannozz at democritos.it Sat May 24 16:12:29 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 24 May 2008 16:12:29 +0200 Subject: [Pw_forum] Error in cppp.x In-Reply-To: References: Message-ID: <55602808-68A4-4758-9711-16E7506431F8@democritos.it> On May 22, 2008, at 16:01 , Ramiro Cardona wrote: > cppp.x < h2o_mol.cppp-dens.in shows the following error: [...] it should be fixed now. Please try the attached modified version Paolo -------------- next part -------------- A non-text attachment was scrubbed... Name: fpmdpp.f90 Type: application/octet-stream Size: 28899 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20080524/51e6f92e/attachment-0001.obj -------------- next part -------------- --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From ramirocardona at gmail.com Sat May 24 17:01:56 2008 From: ramirocardona at gmail.com (Ramiro Cardona) Date: Sat, 24 May 2008 10:01:56 -0500 Subject: [Pw_forum] Error in cppp.x In-Reply-To: <55602808-68A4-4758-9711-16E7506431F8@democritos.it> References: <55602808-68A4-4758-9711-16E7506431F8@democritos.it> Message-ID: Dear Paolo The attached file (fpmdpp.f90) is identical to the file in the original distribution espresso-4.0 Best regards Ramiro Cardona Physics Departament Universidad Nacional de Colombia 2008/5/24 Paolo Giannozzi : > On May 22, 2008, at 16:01 , Ramiro Cardona wrote: > > cppp.x < h2o_mol.cppp-dens.in shows the following error: [...] >> > > it should be fixed now. Please try the attached modified > version > > Paolo > > > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080524/4fda4b5c/attachment.htm From giannozz at democritos.it Sat May 24 18:59:37 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 24 May 2008 18:59:37 +0200 Subject: [Pw_forum] Error in cppp.x In-Reply-To: References: <55602808-68A4-4758-9711-16E7506431F8@democritos.it> Message-ID: On May 24, 2008, at 17:01 , Ramiro Cardona wrote: > The attached file (fpmdpp.f90) is identical to the file > in the original distribution espresso-4.0 oops...I sent the old one. This should be the new one Paolo -------------- next part -------------- A non-text attachment was scrubbed... Name: fpmdpp.f90 Type: application/octet-stream Size: 29843 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20080524/4e65118c/attachment-0001.obj -------------- next part -------------- --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From ramirocardona at gmail.com Sat May 24 19:56:17 2008 From: ramirocardona at gmail.com (Ramiro Cardona) Date: Sat, 24 May 2008 12:56:17 -0500 Subject: [Pw_forum] Error in cppp.x In-Reply-To: References: <55602808-68A4-4758-9711-16E7506431F8@democritos.it> Message-ID: Dear Paolo: The program run OK. No error Thanks a lot for your work Best regards Ramiro Cardona Physics Departament Universidad Nacional de Colombia 2008/5/24 Paolo Giannozzi : > > On May 24, 2008, at 17:01 , Ramiro Cardona wrote: > > The attached file (fpmdpp.f90) is identical to the file >> in the original distribution espresso-4.0 >> > > oops...I sent the old one. This should be the new one > Paolo > > > > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > 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/20080524/102ac981/attachment.htm From giannozz at democritos.it Sat May 24 21:00:40 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 24 May 2008 21:00:40 +0200 Subject: [Pw_forum] Error in cppp.x In-Reply-To: References: <55602808-68A4-4758-9711-16E7506431F8@democritos.it> Message-ID: On May 24, 2008, at 19:56 , Ramiro Cardona wrote: > Dear Paolo: > > The program run OK. No error > > Thanks a lot for your work actually it was only in part mine: http://www.democritos.it:8888/O-sesame/chngview?cn=5934 P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From marzari at MIT.EDU Sat May 24 22:24:30 2008 From: marzari at MIT.EDU (Nicola Marzari) Date: Sat, 24 May 2008 16:24:30 -0400 Subject: [Pw_forum] relaxation In-Reply-To: <4837D884.4030005@sissa.it> References: <577932.94022.qm@web33108.mail.mud.yahoo.com> <4837D884.4030005@sissa.it> Message-ID: <4838797E.9030000@mit.edu> > ali kazempoor wrote: >> Dear All >> for relaxation a surface, i want to fix positions of >> one layer . could you help me how can i do that? Also - does it really help fixing one layer, when all others can move ? (It can, but in fairly exotic circumstances or reasons) nicola -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From baroni at sissa.it Sun May 25 17:05:04 2008 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 25 May 2008 17:05:04 +0200 Subject: [Pw_forum] relaxation In-Reply-To: <4838797E.9030000@mit.edu> References: <577932.94022.qm@web33108.mail.mud.yahoo.com> <4837D884.4030005@sissa.it> <4838797E.9030000@mit.edu> Message-ID: What Ali probably wants to do is ti fix one _interlayer distance_, don't you, Ali? Ali: to elaborate a bit more on Nicola's reply - the position of any individual atom does not matter because of translational invariance (or homogeneity of space, if you prefer). This is what you meant, Nicola, didn't you? Stefano On May 24, 2008, at 10:24 PM, Nicola Marzari wrote: > >> ali kazempoor wrote: >>> Dear All >>> for relaxation a surface, i want to fix positions of >>> one layer . could you help me how can i do that? > > > Also - does it really help fixing one layer, when all others can > move ? > (It can, but in fairly exotic circumstances or reasons) > > nicola > -- > --------------------------------------------------------------------- > Prof Nicola Marzari Department of Materials Science and Engineering > 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA > tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080525/82590e08/attachment.htm From yccheng.nju at gmail.com Mon May 26 05:04:20 2008 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Mon, 26 May 2008 11:04:20 +0800 Subject: [Pw_forum] disagreement of *.in and *.out file in VCSexample Message-ID: Dear pwscf users: I checked VCSexample in V4.0, and found a disagreement in the *.in and *.out. For example: In the As.vcs00.in file,the system is defined as follows: ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + ibrav = 0 , + A = 3.70971016 , + B = 3.70971016 , + C = 3.70971016 , + cosAB = 0.49517470 , + cosAC = 0.49517470 , + cosBC = 0.49517470 , + + CELL_PARAMETERS cubic + 0.58012956 0.00000000 0.81452422 + -0.29006459 0.50240689 0.81452422 + -0.29006459 -0.50240689 0.81452422 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ In the beginning of As.vcs00.out file,the system is changed. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + bravais-lattice index = 0 + lattice parameter (a_0) = 7.0103 a.u. + unit-cell volume = 245.3705 (a.u.)^3 + + celldm(1)= 7.010336 celldm(2)= 1.000000 celldm(3)= 1.000000 + celldm(4)= 0.495175 celldm(5)= 0.000000 celldm(6)= 0.000000 + + crystal axes: (cart. coord. in units of a_0) + a(1) = ( 0.580130 0.000000 0.814524 ) + a(2) = ( -0.290065 0.502407 0.814524 ) + a(3) = ( -0.290065 -0.502407 0.814524 ) +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ a=3.70971016A -> celldm(1)=7.010336a.u. and celldm(2)=celldm(3)=1 celldm(4)=cos(bc)=0.495175 but why celldm(5),celldm(6)are equal to 0? -- Y. C. Cheng Department of Phyics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080526/d5cc82ba/attachment.htm From xylnew at gmail.com Mon May 26 05:47:33 2008 From: xylnew at gmail.com (Y.L. Xie) Date: Mon, 26 May 2008 11:47:33 +0800 Subject: [Pw_forum] disagreement of *.in and *.out file in VCSexample In-Reply-To: References: Message-ID: <1211773653.3044.3.camel@fc7> ? 2008-05-26?? 11:04 +0800? =?GB2312?B?IrPM0620uiIgPHljY2hlbmcubmp1QGdtYWlsLmNvbT4=?=??? > Dear pwscf users: Dear Y. C. Cheng, > I checked VCSexample in V4.0, and found a disagreement in the ^^^^^^ Please ALWAYS check manual before ask question in this forum. > *.in and *.out. For example: > In the As.vcs00.in file,the system is defined as follows: > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > + ibrav = 0 , > + A = 3.70971016 , > + B = 3.70971016 , > + C = 3.70971016 , > + cosAB = 0.49517470 , > + cosAC = 0.49517470 , > + cosBC = 0.49517470 , > + > + CELL_PARAMETERS cubic > + 0.58012956 0.00000000 0.81452422 > + -0.29006459 0.50240689 0.81452422 > + -0.29006459 -0.50240689 0.81452422 > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > In the beginning of As.vcs00.out file,the system is changed. > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > + bravais-lattice index = 0 > + lattice parameter (a_0) = 7.0103 a.u. > + unit-cell volume = 245.3705 (a.u.)^3 > + > + celldm(1)= 7.010336 celldm(2)= 1.000000 celldm(3)= > 1.000000 celldm(2)=b/a,celldm(3)=c/a Best Xie Y.L. > + celldm(4)= 0.495175 celldm(5)= 0.000000 celldm(6)= > 0.000000 > + > + crystal axes: (cart. coord. in units of a_0) > + a(1) = ( 0.580130 0.000000 0.814524 ) > + a(2) = ( -0.290065 0.502407 0.814524 ) > + a(3) = ( -0.290065 -0.502407 0.814524 ) > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > a=3.70971016A -> celldm(1)=7.010336a.u. and celldm(2)=celldm(3)=1 > celldm(4)=cos(bc)=0.495175 > but why celldm(5),celldm(6)are equal to 0? > > -- > Y. C. Cheng > Department of Phyics > Nanjing University > Nanjing 210093 > P. R. China > Tel: 86-25-83592907 > Email: yccheng.nju at gmail.com > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From eariel99 at gmail.com Mon May 26 06:55:52 2008 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Mon, 26 May 2008 00:55:52 -0400 Subject: [Pw_forum] OpenMPI on mac Message-ID: Hi, I am new with Macs. I am learning to compile in it. Frankly, I have been happy after installing fink, so I am still Linux minded. I installed g95, and with it I could compile QE serially. The problem is to use mpif90. There is an mpif90 that comes with Xcode version 3, but it is not configured. When I run it I have this message. Macintosh:Developer eariel$ mpif90 -------------------------------------------------------------------------- Unfortunately, this installation of Open MPI was not compiled with Fortran 90 support. As such, the mpif90 compiler is non-functional. Obviously I would have to configure it, but I do not find any file named configure. Is there an option to reconfigure it within Xcode, without downloading OpenMPI independently of Xcode? Other question, is there a gfortran in Xcode? How to install it? Thanks -- Eduardo Menendez -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080526/9184c53c/attachment.htm From akohlmey at cmm.chem.upenn.edu Mon May 26 06:31:41 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Mon, 26 May 2008 00:31:41 -0400 (EDT) Subject: [Pw_forum] OpenMPI on mac In-Reply-To: References: Message-ID: On Mon, 26 May 2008, Eduardo Ariel Menendez Proupin wrote: EAMP> Hi, EAMP> I am new with Macs. I am learning to compile in it. Frankly, I have been EAMP> happy after installing fink, so I am still Linux minded. I installed g95, EAMP> and with it I could compile QE serially. The problem is to use mpif90. There EAMP> is an mpif90 that comes with Xcode version 3, but it is not configured. When EAMP> I run it I have this message. this is a _very_ mac specific question. have you considered asking at a mac forum? axel. EAMP> EAMP> Macintosh:Developer eariel$ mpif90 EAMP> -------------------------------------------------------------------------- EAMP> Unfortunately, this installation of Open MPI was not compiled with EAMP> Fortran 90 support. As such, the mpif90 compiler is non-functional. EAMP> EAMP> Obviously I would have to configure it, but I do not find any file named EAMP> configure. Is there an option to reconfigure it within Xcode, without EAMP> downloading OpenMPI independently of Xcode? EAMP> EAMP> Other question, is there a gfortran in Xcode? How to install it? EAMP> Thanks EAMP> EAMP> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From yccheng.nju at gmail.com Mon May 26 07:42:32 2008 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Mon, 26 May 2008 13:42:32 +0800 Subject: [Pw_forum] disagreement of *.in and *.out file in VCSexample In-Reply-To: <1211773653.3044.3.camel@fc7> References: <1211773653.3044.3.camel@fc7> Message-ID: Dear Y. L. Xie, I know celldm(2)=b/a,celldm(3)=c/a. My question is why celldm(5) and celldm(6) are equal to 0.495175 in the input file, but equal to 0 in the out file. 2008/5/26, Y.L. Xie : > > ? 2008-05-26?? 11:04 +0800? > =?GB2312?B?IrPM0620uiIgPHljY2hlbmcubmp1QGdtYWlsLmNvbT4=?=??? > > Dear pwscf users: > Dear Y. C. Cheng, > > I checked VCSexample in V4.0, and found a disagreement in the > ^^^^^^ > Please ALWAYS check manual before ask question in this forum. > > > *.in and *.out. For example: > > In the As.vcs00.in file,the system is defined as follows: > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > + ibrav = 0 , > > + A = 3.70971016 , > > + B = 3.70971016 , > > + C = 3.70971016 , > > + cosAB = 0.49517470 , > > + cosAC = 0.49517470 , > > + cosBC = 0.49517470 , > > + > > + CELL_PARAMETERS cubic > > + 0.58012956 0.00000000 0.81452422 > > + -0.29006459 0.50240689 0.81452422 > > + -0.29006459 -0.50240689 0.81452422 > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > In the beginning of As.vcs00.out file,the system is changed. > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > + bravais-lattice index = 0 > > + lattice parameter (a_0) = 7.0103 a.u. > > + unit-cell volume = 245.3705 (a.u.)^3 > > + > > + celldm(1)= 7.010336 celldm(2)= 1.000000 celldm(3)= > > 1.000000 > > celldm(2)=b/a,celldm(3)=c/a > Best > > Xie Y.L. > > > + celldm(4)= 0.495175 celldm(5)= 0.000000 celldm(6)= > > 0.000000 > > + > > + crystal axes: (cart. coord. in units of a_0) > > + a(1) = ( 0.580130 0.000000 0.814524 ) > > + a(2) = ( -0.290065 0.502407 0.814524 ) > > + a(3) = ( -0.290065 -0.502407 0.814524 ) > > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > a=3.70971016A -> celldm(1)=7.010336a.u. and celldm(2)=celldm(3)=1 > > celldm(4)=cos(bc)=0.495175 > > but why celldm(5),celldm(6)are equal to 0? > > > > -- > > Y. C. Cheng > > Department of Phyics > > Nanjing University > > Nanjing 210093 > > P. R. China > > Tel: 86-25-83592907 > > Email: yccheng.nju at gmail.com > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Y. C. Cheng Department of Phyics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080526/77ec2f8e/attachment-0001.htm From xylnew at gmail.com Mon May 26 08:54:59 2008 From: xylnew at gmail.com (Y.L. Xie) Date: Mon, 26 May 2008 14:54:59 +0800 Subject: [Pw_forum] disagreement of *.in and *.out file in VCSexample In-Reply-To: References: <1211773653.3044.3.camel@fc7> Message-ID: <1211784899.3175.3.camel@fc7> Dear Cheng, That is absolutely a bug in the code,for the earlier version can give right output. PWSCF is a free code, please fix it and mail it to developers. Thanks. Xie ? 2008-05-26?? 13:42 +0800? =?GB2312?B?IrPM0620uiIgPHljY2hlbmcubmp1QGdtYWlsLmNvbT4=?=??? > Dear Y. L. Xie, > I know celldm(2)=b/a,celldm(3)=c/a. My question is why > celldm(5) and celldm(6) are equal to 0.495175 in the input file, > but equal to 0 in the out file. > > > 2008/5/26, Y.L. Xie : > ? 2008-05-26?? 11:04 +0800? > =?GB2312?B?IrPM0620uiIgPHljY2hlbmcubmp1QGdtYWlsLmNvbT4=?=? > ?? > > Dear pwscf users: > Dear Y. C. Cheng, > > I checked VCSexample in V4.0, and found a disagreement > in the > ^^^^^^ > Please ALWAYS check manual before ask question in this forum. > > > *.in and *.out. For example: > > In the As.vcs00.in file,the system is defined as follows: > > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > + ibrav = 0 , > > + A = 3.70971016 , > > + B = 3.70971016 , > > + C = 3.70971016 , > > + cosAB = 0.49517470 , > > + cosAC = 0.49517470 , > > + cosBC = 0.49517470 , > > + > > + CELL_PARAMETERS cubic > > + 0.58012956 0.00000000 0.81452422 > > + -0.29006459 0.50240689 0.81452422 > > + -0.29006459 -0.50240689 0.81452422 > > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > In the beginning of As.vcs00.out file,the system is changed. > > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > + bravais-lattice index = 0 > > + lattice parameter (a_0) = 7.0103 a.u. > > + unit-cell volume = 245.3705 (a.u.)^3 > > + > > + celldm(1)= 7.010336 celldm(2)= > 1.000000 celldm(3)= > > 1.000000 > > celldm(2)=b/a,celldm(3)=c/a > Best > > Xie Y.L. > > > + celldm(4)= 0.495175 celldm(5)= > 0.000000 celldm(6)= > > 0.000000 > > + > > + crystal axes: (cart. coord. in units of a_0) > > + a(1) = ( 0.580130 0.000000 0.814524 ) > > + a(2) = ( -0.290065 0.502407 0.814524 ) > > + a(3) = ( -0.290065 -0.502407 0.814524 ) > > > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > a=3.70971016A -> celldm(1)=7.010336a.u. and > celldm(2)=celldm(3)=1 > > celldm(4)=cos(bc)=0.495175 > > but why celldm(5),celldm(6)are equal to 0? > > > > -- > > Y. C. Cheng > > Department of Phyics > > Nanjing University > > Nanjing 210093 > > P. R. China > > Tel: 86-25-83592907 > > Email: yccheng.nju at gmail.com > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > Y. C. Cheng > Department of Phyics > Nanjing University > Nanjing 210093 > P. R. China > Tel: 86-25-83592907 > Email: yccheng.nju at gmail.com > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From degironc at sissa.it Mon May 26 10:44:52 2008 From: degironc at sissa.it (Stefano de Gironcoli) Date: Mon, 26 May 2008 10:44:52 +0200 Subject: [Pw_forum] disagreement of *.in and *.out file in VCSexample In-Reply-To: References: <1211773653.3044.3.camel@fc7> Message-ID: <483A7884.4080604@sissa.it> Dear Y.C. Cheng , when ibrav = 0 (your case) the Bravais lattice vectors are read from the cell_parameters card not build from celldm's or a,b,c,... Only the value of a is used and converted to a.u. the other are not used... You are right that there is a bug in the sense that the code should stop and complain that you are providing not needed information (or set all celldm(2:5) to zero and continue) best regards. stefano de Gironcoli ??? wrote: > Dear Y. L. Xie, > I know celldm(2)=b/a,celldm(3)=c/a. My question is why > celldm(5) and celldm(6) are equal to 0.495175 in the input file, > but equal to 0 in the out file. > > > 2008/5/26, Y.L. Xie >: > > ? 2008-05-26?? 11:04 +0800? > =?GB2312?B?IrPM0620uiIgPHljY2hlbmcubmp1QGdtYWlsLmNvbT4=?=??? > > Dear pwscf users: > Dear Y. C. Cheng, > > I checked VCSexample in V4.0, and found a disagreement in the > ^^^^^^ > Please ALWAYS check manual before ask question in this forum. > > > *.in and *.out. For example: > > In the As.vcs00.in file,the system is > defined as follows: > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > + ibrav = 0 , > > + A = 3.70971016 , > > + B = 3.70971016 , > > + C = 3.70971016 , > > + cosAB = 0.49517470 , > > + cosAC = 0.49517470 , > > + cosBC = 0.49517470 , > > + > > + CELL_PARAMETERS cubic > > + 0.58012956 0.00000000 0.81452422 > > + -0.29006459 0.50240689 0.81452422 > > + -0.29006459 -0.50240689 0.81452422 > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > In the beginning of As.vcs00.out file,the system is changed. > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > + bravais-lattice index = 0 > > + lattice parameter (a_0) = 7.0103 a.u. > > + unit-cell volume = 245.3705 (a.u.)^3 > > + > > + celldm(1)= 7.010336 celldm(2)= 1.000000 celldm(3)= > > 1.000000 > > celldm(2)=b/a,celldm(3)=c/a > Best > > Xie Y.L. > > > + celldm(4)= 0.495175 celldm(5)= 0.000000 celldm(6)= > > 0.000000 > > + > > + crystal axes: (cart. coord. in units of a_0) > > + a(1) = ( 0.580130 0.000000 0.814524 ) > > + a(2) = ( -0.290065 0.502407 0.814524 ) > > + a(3) = ( -0.290065 -0.502407 0.814524 ) > > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > a=3.70971016A -> celldm(1)=7.010336a.u. and celldm(2)=celldm(3)=1 > > celldm(4)=cos(bc)=0.495175 > > but why celldm(5),celldm(6)are equal to 0? > > > > -- > > Y. C. Cheng > > Department of Phyics > > Nanjing University > > Nanjing 210093 > > P. R. China > > Tel: 86-25-83592907 > > Email: yccheng.nju at gmail.com > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > Y. C. Cheng > Department of Phyics > Nanjing University > Nanjing 210093 > P. R. China > Tel: 86-25-83592907 > Email: yccheng.nju at gmail.com > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From giannozz at democritos.it Mon May 26 11:01:55 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 26 May 2008 11:01:55 +0200 Subject: [Pw_forum] OpenMPI on mac In-Reply-To: References: Message-ID: <483A7C83.2090000@democritos.it> Eduardo Ariel Menendez Proupin wrote: > I am new with Macs. [...] Is there an option to reconfigure it within > Xcode, without downloading OpenMPI independently of Xcode? you may have better luck if you download and compile openmpi: it is relatively easy > Other question, is there a gfortran in Xcode? How to install it? I used binaries here: http://gcc.gnu.org/wiki/GFortranBinaries . Only very recent versions of gfortran work for q-e Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From aryjunior at gmail.com Mon May 26 20:23:12 2008 From: aryjunior at gmail.com (Ary Junior) Date: Mon, 26 May 2008 15:23:12 -0300 Subject: [Pw_forum] GIPAW compilation Message-ID: <4c9c61c20805261123gdcdbff2m2259cf6f93e95e4@mail.gmail.com> Hi, Im trying to compile GIPAW with Intel Fortran Compiler. Before it I do: export PATH=/opt/intel/fc/10.1.008/bin:$PATH And when I execute the make commad, after many steps i get the error: /usr/bin/ld.real: cannot find -lessl make: *** [gipaw.x] Error 1 Anybody can help me? Thanks very much!!! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080526/fbc0533e/attachment.htm From paulatto at sissa.it Mon May 26 21:13:02 2008 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 26 May 2008 21:13:02 +0200 (CEST) Subject: [Pw_forum] GIPAW compilation In-Reply-To: <4c9c61c20805261123gdcdbff2m2259cf6f93e95e4@mail.gmail.com> References: <4c9c61c20805261123gdcdbff2m2259cf6f93e95e4@mail.gmail.com> Message-ID: <27889.82.52.175.127.1211829182.squirrel@webmail.sissa.it> On Mon, May 26, 2008 20:23, Ary Junior wrote: > export PATH=/opt/intel/fc/10.1.008/bin:$PATH Hi, ifort requires more than one variable to work correctly, there is a script which set up all the required variables correctly in /opt/intel/fc/*/bin/, if I remember correctly it is named ifortvars.sh. You can copy the script in /etc/profile.d/ in order to make it global and permanent (requires a relogin to take effect), or just execute it when you need to use ifort typing source /opt/intel/fc/*/bin/*vars.sh I hope it helps, bye -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) +39 040 3787 511 http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From akohlmey at cmm.chem.upenn.edu Mon May 26 20:59:44 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Mon, 26 May 2008 14:59:44 -0400 (EDT) Subject: [Pw_forum] GIPAW compilation In-Reply-To: <4c9c61c20805261123gdcdbff2m2259cf6f93e95e4@mail.gmail.com> References: <4c9c61c20805261123gdcdbff2m2259cf6f93e95e4@mail.gmail.com> Message-ID: On Mon, 26 May 2008, Ary Junior wrote: hi ary! AJ> Hi, Im trying to compile GIPAW with Intel Fortran Compiler. Before it I do: AJ> AJ> export PATH=/opt/intel/fc/10.1.008/bin:$PATH AJ> AJ> And when I execute the make commad, after many steps i get the error: AJ> AJ> /usr/bin/ld.real: cannot find -lessl AJ> make: *** [gipaw.x] Error 1 hmmm... this looks strange. did you run ./configure first? if yes, how come you have a reference to ESSL in your make.sys file as this is only available on IBM cpus (for which in turn no intel compiler exists). please re-read the QE installation procedure and try again. ...and then provide more details about what you did and what did or did not work etc. cheers, axel. AJ> AJ> Anybody can help me? AJ> AJ> Thanks very much!!! AJ> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From akohlmey at cmm.chem.upenn.edu Mon May 26 21:05:11 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Mon, 26 May 2008 15:05:11 -0400 (EDT) Subject: [Pw_forum] GIPAW compilation In-Reply-To: <27889.82.52.175.127.1211829182.squirrel@webmail.sissa.it> References: <4c9c61c20805261123gdcdbff2m2259cf6f93e95e4@mail.gmail.com> <27889.82.52.175.127.1211829182.squirrel@webmail.sissa.it> Message-ID: On Mon, 26 May 2008, Lorenzo Paulatto wrote: LP> LP> On Mon, May 26, 2008 20:23, Ary Junior wrote: LP> > export PATH=/opt/intel/fc/10.1.008/bin:$PATH LP> LP> Hi, LP> ifort requires more than one variable to work correctly, there is a script LP> which set up all the required variables correctly in /opt/intel/fc/*/bin/, LP> if I remember correctly it is named ifortvars.sh. lorenzo, that is only true for the default installation instructions, it can actually be made to work the way it is presented and thus you can have multiple versions of the intel compiler installed. speaking of versions. the intel compiler version 10.1.008 is _horribly_ broken and miscompiles a lot of codes (i have proof for CP2K and CPMD) and needs to be updated in any case. cheers, axel. LP> LP> You can copy the script in /etc/profile.d/ in order to make it global and LP> permanent (requires a relogin to take effect), or just execute it when you LP> need to use ifort typing LP> source /opt/intel/fc/*/bin/*vars.sh LP> LP> I hope it helps, bye LP> LP> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From yccheng.nju at gmail.com Tue May 27 05:05:15 2008 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Tue, 27 May 2008 11:05:15 +0800 Subject: [Pw_forum] symmetry changed in vc-relaxation Message-ID: Dear pwscf users: I performed vc-relaxation of SnO2 which has ibrav=6 sysmmetry(a=b!=c,cosab=cosbc=cosac=0). After the relaxation,the symmtry changed(a=b!=c,cosab!=0,cosbc=cosac=0). Is this the code bug? -- Y. C. Cheng Department of Phyics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080527/a98bf5cb/attachment.htm From akohlmey at cmm.chem.upenn.edu Tue May 27 04:40:35 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Mon, 26 May 2008 22:40:35 -0400 (EDT) Subject: [Pw_forum] symmetry changed in vc-relaxation In-Reply-To: References: Message-ID: On Tue, 27 May 2008, wrote: YCC> Dear pwscf users: YCC> I performed vc-relaxation of SnO2 which has ibrav=6 YCC> sysmmetry(a=b!=c,cosab=cosbc=cosac=0). After the relaxation,the symmtry YCC> changed(a=b!=c,cosab!=0,cosbc=cosac=0). YCC> Is this the code bug? or with your input parameters (is the stress tensor converged?), the symmetry is not stable? axel. YCC> YCC> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From degironc at sissa.it Tue May 27 11:50:34 2008 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 27 May 2008 11:50:34 +0200 Subject: [Pw_forum] symmetry changed in vc-relaxation In-Reply-To: References: Message-ID: <483BD96A.10001@sissa.it> Dear YC Cheng, was the symmetry recognized by the code at the beginning of the run and then got lost in the relaxation ... or instead the symmetry was not recognized and then, for numerical or physical reasons, it was not kept ? In the latter case it is either a numerical issue as Axel was suggesting or a real instability of your system toward lower symmetry. In the former case it may be a problem in the vc-relax part. please clarify the situation and provide an example if relevant. Stefano de Gironcoli - SISSA and DEMOCRITOS ??? wrote: > Dear pwscf users: > I performed vc-relaxation of SnO2 which has ibrav=6 > sysmmetry(a=b!=c,cosab=cosbc=cosac=0). After the relaxation,the > symmtry changed(a=b!=c,cosab!=0,cosbc=cosac=0). > Is this the code bug? > > -- > Y. C. Cheng > Department of Phyics > Nanjing University > Nanjing 210093 > P. R. China > Tel: 86-25-83592907 > Email: yccheng.nju at gmail.com > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From holger.hesske at chem.ethz.ch Wed May 28 10:39:55 2008 From: holger.hesske at chem.ethz.ch (Holger Hesske) Date: Wed, 28 May 2008 10:39:55 +0200 Subject: [Pw_forum] Problem in Ionic relaxation and MD runs Message-ID: <200805281039.56092.holger.hesske@chem.ethz.ch> Dear pwscf-users, -developers and other readers, Currently I calculate BaO bulk (and surface) systems. Therefore I use a testsystem with a cubic unitcell containing 8 atoms. Varying the cell length continously (in separate scf calculations (5.00-6.00 Angstrom)) gives a minimum at 5.460 Angstrom, which is 1.1% less then expt. X-ray data and therfore acceptable (or not?). Btw: a reference stated BaO cell length with PBE functional to be 5.59 One of my input files is given below: &control calculation='scf' restart_mode='from_scratch', pseudo_dir = '/cluster/home/chab/hesskeh/pseudo', outdir='/cluster/work/chab/hesskeh/BaO_bulk/CELL_ABC_USPP', disk_io = 'high', / &system ibrav = 0, A = 5.400, B = 5.400, C = 5.400, cosAB = 0, cosAC = 0, cosBC = 0, nat = 8, ntyp = 2, ecutwfc = 50, ecutrho = 400, / &electrons conv_thr = 1.0d-8, mixing_beta = 0.7, startingwfc= 'atomic+random', / CELL_PARAMETERS 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOMIC_SPECIES Ba 137.427 Ba.pbe-nsp-van.UPF O 16.000 O.pbe-van_ak.UPF ATOMIC_POSITIONS Ba 0.000 0.000 0.000 Ba 0.500 0.500 0.000 Ba 0.500 0.000 0.500 Ba 0.000 0.500 0.500 O 0.500 0.000 0.000 O 0.000 0.500 0.000 O 0.000 0.000 0.500 O 0.500 0.500 0.500 K_POINTS automatic 5 5 5 0 0 0 so far so good. Moving on to ionic relaxation (nosym =.true , remove_rigid_rot=.true. ) : (1) Starting from ideal atomic positions the forces where below 3.4D-6 (which is expected) (2) Distortion of one O-atom (O8) from {0.5 0.5 0.5} to {0.45 0.5 0.5} led to force on O8 pointing to -x 0 0, so the distance between Ba and O will be further decrease? (No ionic movement with the default forc_conv_thr) (3) Reducing forc_conv_thr to 1D-4 led to movement of ions but it seems not to converge. (I stopped the calculation after 100 steps of bfgs or damped dynamics and the position of the atoms seemed to be similar and not very different (+-0.002 crystal coordinates) from starting positions) (4) Distortion of O8 to {0.25 0.5 0.5} or {0.75 0.5 0.5} led in the first step of bfgs to a force on the atom pointing to the "right" positions but from the second bfgs step the force on O8 is again the "wrong" direction (see below). The calculation did not converge and O8 move +-0.02 around its starting positions BFGS (1 Step) atom 1 type 1 force = -0.00099130 -0.00000711 -0.00000713 atom 2 type 1 force = -0.00364813 0.00000905 0.00000915 atom 3 type 1 force = -0.00364847 0.00000904 0.00000910 atom 4 type 1 force = -0.48689518 -0.00000708 -0.00000718 atom 5 type 2 force = -0.00003749 0.00000905 0.00000911 atom 6 type 2 force = 0.00461601 -0.00000709 -0.00000715 atom 7 type 2 force = 0.00461686 -0.00000710 -0.00000714 atom 8 type 2 force = 0.48598771 0.00000122 0.00000124 Total force = 0.687983 Total SCF correction = 0.000091 ATOMIC_POSITIONS (after 1 Step) Ba -0.000033151 -0.000000237 -0.000000502 Ba 0.499743037 0.500000638 0.00000644 Ba 0.499743013 0.00000637 0.500000641 Ba -0.034295409 0.499999501 0.499999495 O 0.499997359 0.000000638 0.000000642 O 0.000325137 0.499999501 -0.000000504 O 0.000325197 -0.000000500 0.499999497 O 0.284231490 0.500000086 0.500000088 BFGS (2 Step) atom 1 type 1 force = 0.01415644 -0.00216324 -0.00216320 atom 2 type 1 force = -0.03044379 0.00262967 0.00263000 atom 3 type 1 force = -0.03044377 0.00263004 0.00262963 atom 4 type 1 force = 0.14450759 -0.00226772 -0.00226767 atom 5 type 2 force = 0.00932027 0.00263080 0.00263076 atom 6 type 2 force = -0.01123409 -0.00216209 -0.00216194 atom 7 type 2 force = -0.01123442 -0.00216198 -0.00216206 atom 8 type 2 force = -0.08462822 0.00086451 0.00086449 Total force = 0.174697 Total SCF correction = 0.000033 The question arises: where is the failure or what did I wrong? Or even better: what should I do to get a working relaxation? (Caused by these confusing results I calculate scf's of the BaO cell with 2.6-2.8 angstrom cell length and the total energy was even lower than the "minimum" at 5.46) Maybe with the answer of the question above the next part might be unimportant or useless. But: Starting md's from ideal atomic positions (with and without temp rescaling, dt ={2, 5, 10, 15, 20}) it always ended up finally with pairs of BaO having a interatomic distance below 1.3 Angstrom! I guess it is the same problem... Thanks for reading the complete text and in advance for every hint I get. best regards Holger Hesske PS. I could provide a lot of input and output files but i dont want to waste the time of the readers, in case I made a simple (stupid) mistake in setting up the calculations. -- Dr. Holger Hesske Inst.f.Chemie-/Bioingenieurwissenschaft. Wolfgang-Pauli-Str. 10 ETH H?nggerberg, HCI E 133 CH-8093 Z?rich Tel: +41 44 633 66 19 Fax: +41 44 632 11 63 E-Mail: holger.hesske at chem.ethz.ch From anjmanqi at yahoo.com.cn Wed May 28 15:48:26 2008 From: anjmanqi at yahoo.com.cn (jiming an) Date: Wed, 28 May 2008 21:48:26 +0800 (CST) Subject: [Pw_forum] from ld1_setup : error # 2; mismatched all-electron/pseudo occupations Message-ID: <17594.33059.qm@web15001.mail.cnb.yahoo.com> Dear authors of PWscf, I try use ld1.x to generate pseudo potential of Sb atom. Here is the input file script, -------------------------------------------------------------------------------------------------- &input title='Sb', zed=51., rel=2, rlderiv=2.80, eminld=-5.0, emaxld=5.0, deld=0.02, nld=5, iswitch=3, config='[Kr] 5s2 4d10 5p3 ' dft='PBE', / &inputp pseudotype=3, lloc=0, file_pseudopw='Sbrel.RRKJ3', / 7 4D 3 2 4.00 0.00 2.60 2.60 1.50 4D 3 2 0.00 0.00 2.60 2.60 1.50 4D 3 2 6.00 0.00 2.60 2.60 2.50 4D 3 2 0.00 0.00 2.60 2.60 2.50 5P 4 1 2.00 0.00 2.60 2.60 0.50 5P 4 1 1.00 0.00 2.60 2.60 1.50 5S 1 0 2.00 0.00 2.60 2.60 0.50 ------------------------------------------------------------------------------------------------------------ And the stopping message is: --------------------------------------------------------------------------------------------------------------- program ld1 starts. version 3.2.3 today is 28May2008 at 10:51:31 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from ld1_setup : error # 2 mismatched all-electron/pseudo occupations %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... ------------------------------------------------------------------------------------------------------------------------------------------------ Where is the wrong of the input file? Thank you. Jiming An ___________________________________________________________ ???????????? http://cn.mail.yahoo.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080528/38212a29/attachment.htm From akohlmey at cmm.chem.upenn.edu Wed May 28 16:15:08 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 28 May 2008 10:15:08 -0400 (EDT) Subject: [Pw_forum] Problem in Ionic relaxation and MD runs In-Reply-To: <200805281039.56092.holger.hesske@chem.ethz.ch> References: <200805281039.56092.holger.hesske@chem.ethz.ch> Message-ID: On Wed, 28 May 2008, Holger Hesske wrote: HH> Dear pwscf-users, -developers and other readers, holger, [...] HH> Maybe with the answer of the question above the next part might be unimportant HH> or useless. But: Starting md's from ideal atomic positions (with and without HH> temp rescaling, dt ={2, 5, 10, 15, 20}) it always ended up finally with pairs HH> of BaO having a interatomic distance below 1.3 Angstrom! I guess it is the HH> same problem... HH> HH> Thanks for reading the complete text and in advance for every hint I get. could be you have a crappy Ba potential. is that one using the original data from the vanderbilt site? that is one of the dacapo parameter sets, right? you may need to "tune" the potential fit parameters to get something reasonable. at least that is my experience with most of those parameter sets. if you run the pseudopotential generation code on them, they usually have large "negative densities" and one has to correct for those by adding constraints to the potential fitting (or generate a better potential from scratch). cheers, axel. HH> HH> best regards HH> HH> Holger Hesske HH> HH> PS. I could provide a lot of input and output files but i dont want to waste HH> the time of the readers, in case I made a simple (stupid) mistake in setting HH> up the calculations. HH> HH> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From sks.jnc at gmail.com Thu May 29 07:27:48 2008 From: sks.jnc at gmail.com (S. K. S.) Date: Thu, 29 May 2008 10:57:48 +0530 Subject: [Pw_forum] nelup and neldw Message-ID: Dear all, The fixed occupations and lsda need nelup and neldw, and the phonon code with constrained magnetization is not yet available. Does it imply that the phonon calculation is not possible for fixed occupations and lsda???? regards, S. K. Saha JNCASR BANGALORE -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080529/9b526b28/attachment.htm From Adriano.Mosca.Conte at roma2.infn.it Thu May 29 10:21:58 2008 From: Adriano.Mosca.Conte at roma2.infn.it (Adriano.Mosca.Conte at roma2.infn.it) Date: Thu, 29 May 2008 10:21:58 +0200 (CEST) Subject: [Pw_forum] nelup and neldw In-Reply-To: References: Message-ID: <1248.82.59.196.26.1212049318.squirrel@82.59.196.26> Dear SKS, I read the question that you posed on the pwforum. I would like to stress the fact that nelup and neldw flags are only usful for isolated molecules or atoms in which you have not k-points. and also for isolated molecules it is not always necessary to use it; for example for the double decker I didn't use this machinery. It was only necessary for Tb_2 an TbAu that are systems with lot of states near the Fermi Energy and therefore really difficult to make converge. If you want I can try to find an input of TbF3 that is a molecular solid or at least an output in such a way to reconstruct the input to make the tests. This is a much easier system to treat. I only nead a few hours because this morning I am really buisy but I should be able to send you the input later together with the nonmagnetic Tb_2 (I hope! As I said it is not an easy system to treat). Adriano > Dear all, > > The fixed occupations and lsda need nelup and neldw, and > the phonon code with constrained magnetization is not yet available. > Does it imply that the phonon calculation is not possible > for fixed occupations and lsda???? > > > regards, > S. K. Saha > JNCASR > BANGALORE > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From sks.jnc at gmail.com Thu May 29 10:56:54 2008 From: sks.jnc at gmail.com (S. K. S.) Date: Thu, 29 May 2008 14:26:54 +0530 Subject: [Pw_forum] not an easy system to treat Message-ID: Dear Adriano, Thanks a lot for your kind help. I'll wait for your next reply. regards, SKS JNCASR -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080529/90512d69/attachment.htm From amosleffler at sbcglobal.net Thu May 29 18:42:54 2008 From: amosleffler at sbcglobal.net (Amos Leffler) Date: Thu, 29 May 2008 09:42:54 -0700 Subject: [Pw_forum] GIPAW compilation Message-ID: <3B35A6750ED94E158CB33E9BB3A6DD8A@leffler2> Hi pwscf users, I found in the www.g95.org web site a message from Guglielmo Pasa with directions for configuring mpich2-1.0.1 with g95. It seems simple and I wonder if it would work with the Intel Fortrn compiler? Amos Leffler P.S. Is there a newer version than the 10.1 version? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080529/21a6c76a/attachment.htm From akohlmey at cmm.chem.upenn.edu Thu May 29 19:36:30 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Thu, 29 May 2008 13:36:30 -0400 (EDT) Subject: [Pw_forum] GIPAW compilation In-Reply-To: <3B35A6750ED94E158CB33E9BB3A6DD8A@leffler2> References: <3B35A6750ED94E158CB33E9BB3A6DD8A@leffler2> Message-ID: On Thu, 29 May 2008, Amos Leffler wrote: AL> Hi pwscf users, amos, AL> I found in the www.g95.org web site a message from Guglielmo AL> Pasa with directions for configuring mpich2-1.0.1 with g95. It AL> seems simple and I wonder if it would work with the Intel Fortrn AL> compiler? actually, i would not recommend this strategy. using -fno-underscoring has the high risk that fortran subroutine names may collide with those from c based c-libraries, e.g. the system libc. nevertheless, compiling OpenMPI is just as simple. here is how i compile a custom version with the intel compilers to be installed in my home directory... that one is actually much simpler _and_ compatible to g95 as well (at least for cp2k). env F77=ifort FC=ifort FCFLAGS="-i-static -tpp6 -pc64 -O2" \ FFLAGS="-i-static -tpp6 -pc64 -O2" ./configure --prefix=${HOME}/openmpi \ --enable-orterun-prefix-by-default make && make install to use this install with g95 you just set the environment variables OMPI_FC and OMPI_F77 to g95. AL> Amos Leffler AL> P.S. Is there a newer version than the 10.1 version? you have to check the patch levels. intel constantly updates their releases and at some point in time they tend to converge to something that is more or less reliable. cheers, axel. -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From shrek_826 at yahoo.com.cn Sat May 31 04:30:46 2008 From: shrek_826 at yahoo.com.cn (Fan Yang) Date: Sat, 31 May 2008 10:30:46 +0800 (CST) Subject: [Pw_forum] About PWgui-4.0 and XCrySDen Message-ID: <674993.61975.qm@web15303.mail.cnb.yahoo.com> Dear everyone, ????????I have?two questions about the additional tools?for espresso-4.0. First is the compilation of PWgui-4.0,?namely, when executing ./pwui I?got error message: Can't find package Itcl while executing. ?????? The second is about XCrySDen, when runing espresso-4.0, it seems that only the initial structure?could be displayed,?while the subsequent configurations could not be imported.?If I use the?previous version, espresso-3.2.3, then everything?goes well. ?????? Does anyone?have the?same problem? ?????? Best Regards, ? ====================================== Fan Yang PH.D Candidate?in Electrochemistry????????????????????? College of Chemistry and Molecular Science??????????? Wuhan University,430072,Hubei Province,China? E-mail:shrek_826 at yahoo.com.cn ====================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080531/92ad4b0e/attachment.htm From hqzhou at nju.edu.cn Sat May 31 07:12:33 2008 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Sat, 31 May 2008 13:12:33 +0800 Subject: [Pw_forum] About PWgui-4.0 and XCrySDen References: <674993.61975.qm@web15303.mail.cnb.yahoo.com> Message-ID: <006301c8c2dc$ef96a4c0$a600a8c0@solarflare> You need to do right as the error message told you. A longer name for Itcl is [incr Tcl] and it's an extension to the Tcl language. Go to download and install the package. www.activestate.com should be a good place. The standard edition is for free. Dr. Huiqun Zhou @Nanjing University, China ----- Original Message ----- From: Fan Yang To: pw_forum at pwscf.org Sent: Saturday, May 31, 2008 10:30 AM Subject: [Pw_forum] About PWgui-4.0 and XCrySDen Dear everyone, I have two questions about the additional tools for espresso-4.0. First is the compilation of PWgui-4.0, namely, when executing ./pwui I got error message: Can't find package Itcl while executing. The second is about XCrySDen, when runing espresso-4.0, it seems that only the initial structure could be displayed, while the subsequent configurations could not be imported. If I use the previous version, espresso-3.2.3, then everything goes well. Does anyone have the same problem? Best Regards, ====================================== Fan Yang PH.D Candidate in Electrochemistry College of Chemistry and Molecular Science Wuhan University,430072,Hubei Province,China E-mail:shrek_826 at yahoo.com.cn ====================================== ------------------------------------------------------------------------------ _______________________________________________ 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/20080531/6c95e884/attachment.htm From madhura at jncasr.ac.in Sat May 31 08:14:56 2008 From: madhura at jncasr.ac.in (Madhura Marathe) Date: Sat, 31 May 2008 11:44:56 +0530 (IST) Subject: [Pw_forum] About PWgui-4.0 and XCrySDen In-Reply-To: <674993.61975.qm@web15303.mail.cnb.yahoo.com> References: <674993.61975.qm@web15303.mail.cnb.yahoo.com> Message-ID: <40394.172.16.1.1.1212214496.squirrel@172.16.1.1> Hi, I had encountered the same problem with Xcrysden. It occurs because of change in output format for the latest version. Earlier versions will print only relaxed atomic positions (x, y and z coords), but in 4.0 version the relaxed positions are followed by input parameters specified in input file for relaxing atoms (0 or 1). Hence Xcrysden cannot read these and shows only initial configuration which is in usual format. If you remove extra three no.s in each atomic positions from the output file, it works fine. -Madhura. > Dear everyone, > I have two questions about the additional tools for espresso-4.0. > First is the compilation of PWgui-4.0, namely, when executing ./pwui > I got error message: Can't find package Itcl while executing. > The second is about XCrySDen, when runing espresso-4.0, it seems > that only the initial structure could be displayed, while the subsequent > configurations could not be imported. If I use the previous version, > espresso-3.2.3, then everything goes well. > Does anyone have the same problem? > Best Regards, > > > =====================================Fan Yang > PH.D Candidate in Electrochemistry > College of Chemistry and Molecular Science > Wuhan University,430072,Hubei Province,China > E-mail:shrek_826 at yahoo.com.cn > =================================== > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Madhura Marathe, PhD student, TSU, JNCASR, Bangalore. India. From paulatto at sissa.it Sat May 31 09:09:23 2008 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Sat, 31 May 2008 09:09:23 +0200 (CEST) Subject: [Pw_forum] About PWgui-4.0 and XCrySDen In-Reply-To: <674993.61975.qm@web15303.mail.cnb.yahoo.com> References: <674993.61975.qm@web15303.mail.cnb.yahoo.com> Message-ID: <20155.82.48.141.31.1212217763.squirrel@webmail.sissa.it> On Sat, May 31, 2008 04:30, Fan Yang wrote: > Dear everyone, > I have two questions about the additional tools for espresso-4.0. > First is the compilation of PWgui-4.0, namely, when executing ./pwui > I got error message: Can't find package Itcl while executing. You have to install itcl and iwidgets, which are extensions to tcl. You have better stick to you linux distribution's packages, if available. > Does anyone have the same problem? I can't check now, are you using version 1.4 or the latest snapshot? The latter is much more compatible with QE 4.0. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) +39 040 3787 511 http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From bogus@does.not.exist.com Wed May 14 11:32:07 2008 From: bogus@does.not.exist.com () Date: Wed, 14 May 2008 09:32:07 -0000 Subject: No subject Message-ID: The phonon code with LDA+U is not yet available I infer from the use of the adverb "yet" that such code is in the works? I see anticipatory flags exist phq_readin.f90. I could really use such a feature and would be quite willing to help create and test it. -Paul Paul M. Grant, PhD Principal, W2AGZ Technologies Visiting Scholar, Applied Physics, Stanford University EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus w2agz at pacbell.net http://www.w2agz.com ------=_NextPart_000_0001_01C8CC25.A0679BA0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable phq_readin and LDA+U

To = All:

I just tried = running ph.x on the scf output of some runs on = antiferromagnetic transition metal = oxides and got = the following message:

From phq_readin = error # 1

The phonon code = with LDA+U is = not yet available

I infer from = the use of the adverb “yet” that such code is in the works?  I see = anticipatory flags exist phq_readin.f90.

I could really = use such a feature and would be quite willing to help create and test = it.

-Paul

Paul M. Grant, = PhD

Principal, W2AGZ = Technologies

Visiting Scholar, Applied = Physics, Stanford University

EPRI Science Fellow = (Retired)

IBM Research Staff Member = Emeritus

w2agz at pacbell.net

http://www.w2agz.com

 

 

------=_NextPart_000_0001_01C8CC25.A0679BA0-- From bogus@does.not.exist.com Wed May 14 11:32:07 2008 From: bogus@does.not.exist.com () Date: Wed, 14 May 2008 09:32:07 -0000 Subject: No subject Message-ID: The value remain the same when calculate by same number of CPUs and pools. There would be only a little different for different number of CPUs and pools, less than 0.01% in energy. K-point mesh Pseudopotentials Cutoff / Ry Anatase lattice parameters time a=b c Energy / Ry CPU Wall experiment* x 3.78216 9.50465 x x x CASTEP 400 eV 3.7987 9.6934 -730.11745 gamma (1X1X1) 30,240 3.39021 11.77804 -725.08174 4m18.70s 18m 9.12s 2X2X1 30??240 3.8683 9.0275 -725.48834 8m 4.25s 32m33.56s 4X4X2 25,200 3.7500 9.3829 -725.41398 9m58.82s 17m46.87s 30,240 3.7899 9.6203 -725.49520 3m41.55s 7m50.32s 40,320 3.7850 9.5716 -725.54336 8m54.73s 34m 1.43s 50,400 3.7926 9.6366 -725.59434 10m14.46s 41m 3.22s 7X7X3 30,240 3.7919 9.6058 -725.49443 31m59.60s 46m37.77s 10X10X4 30,240 3.7916 9.6067 -725.49451 31m32.94s 44m 4.11s The input file as follows, &CONTROL title = 'Anatase lattice' , calculation = 'vc-relax' , restart_mode = 'from_scratch' , outdir = '/home/vega/espresso-4.0/tmp/' , wfcdir = '/tmp/' , pseudo_dir = '/home/vega/espresso-4.0/pseudo/' , prefix = 'Anatase lattice default' , disk_io = 'none' , etot_conv_thr = 0.0005 , forc_conv_thr = 0.0011668141375 , nstep = 1000 , / &SYSTEM ibrav = 6, celldm(1) = 7.1356, celldm(3) = 2.5122, nat = 12, ntyp = 2, ecutwfc = 30 , ecutrho = 240 , / &ELECTRONS conv_thr = 7.3D-8 , / &IONS ion_dynamics = 'bfgs' , / &CELL cell_dynamics = 'bfgs' , / ATOMIC_SPECIES Ti 47.86700 Ti.pw91-sp-van_ak.UPF O 15.99940 O.pw91-van_ak.UPF ATOMIC_POSITIONS crystal Ti 0.000000000 0.000000000 0.000000000 Ti 0.500000000 0.500000000 0.500000000 Ti 0.000000000 0.500000000 0.250000000 Ti 0.500000000 0.000000000 0.750000000 O 0.000000000 0.500000000 0.042000000 O 0.000000000 0.000000000 0.208000000 O 0.500000000 0.500000000 0.292000000 O 0.000000000 0.500000000 0.458000000 O 0.500000000 0.000000000 0.542000000 O 0.500000000 0.500000000 0.708000000 O 0.000000000 0.000000000 0.792000000 O 0.500000000 1.000000000 0.958000000 K_POINTS automatic 2 2 1 1 1 1 But it is especially strange that the total energy was -730.11745 Ry, rather different than the PWscf's results. Also PWscf's results seems to be a litter lager than experimental data. Is it because the pseudopotential Ti.pw91-sp-van_ak.UPF underbinding for TiO2? Vega Lew PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China _________________________________________________________________ Discover the new Windows Vista http://search.msn.com/results.aspx?q=windows+vista&mkt=en-US&form=QBRE From bogus@does.not.exist.com Wed May 14 11:32:07 2008 From: bogus@does.not.exist.com () Date: Wed, 14 May 2008 09:32:07 -0000 Subject: No subject Message-ID: self-consistent calculation with E=0 and E=0.001a.u. (E is an external homogeneous electric field), we can get esp_{inf} i.e. the ions do not respond to the electric field. Now since I want to calculate esp_0 (include the response of ions), I relax all the atoms by using 'relax'. However, I found that all the forces on the atoms are zero even if I turn on electric field. So how to calculate static dielectric field (esp_0) ? Why are the forces zero even when the external electric is turned on? Thank you very much. Hanghui Department of Physics Yale University ------=_Part_42881_24643191.1216773250655 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear PWSCF users,
      I am now trying to calculate the static dielectric constant (esp_0). From the example31 in the espresso4.0 package, I know that by doing two self-consistent calculation with E=0 and E=0.001a.u. (E is an external homogeneous electric field), we can get esp_{inf} i.e. the ions do not respond to the electric field. Now since I want to calculate esp_0 (include the response of ions), I relax all the atoms by using 'relax'. However, I found that all the forces on the atoms are zero even if I turn on electric field. So how to calculate static dielectric field (esp_0) ? Why are the forces zero even when the external electric is turned on?
      Thank you very much.
 
Hanghui
Department of Physics
Yale University
------=_Part_42881_24643191.1216773250655-- From bogus@does.not.exist.com Wed May 14 11:32:07 2008 From: bogus@does.not.exist.com () Date: Wed, 14 May 2008 09:32:07 -0000 Subject: No subject Message-ID: When (nrc<0) or (nrc>msh). I think there is something wrong with the paw pseudopotential or some important parameters have been neglected in the input file for g-tensor calculation. I have not found any clues about this error in the forum. Any suggestions or examples for g-tensor calculation will be deeply appreciated. the details of the input files: ----------------------------- scf input file -------------------------- &control calculation = 'scf', prefix='zro2', restart_mode='from_scratch', pseudo_dir = '/usr/local/espresso-4.0/g-tensor/pseudo/', outdir='./', dt=80, verbosity=default, etot_conv_thr=1.0D-5, forc_conv_thr=1.0D-4, nstep=50, / &system ibrav= 0, celldm(1)=10.323, nat= 11, ntyp= 2, ecutwfc = 30.0, ecutrho = 300.0, occupations = "smearing", smearing = "gaussian", degauss = 0.02D0, / &electrons conv_thr = 1.D-6, mixing_beta = 0.3D0, / CELL_PARAMETERS 1.00 0.000000000 0.000000000 0.000000000 1.00 0.000000 0.000000000 0.000000 1.00 ATOMIC_SPECIES Zr1 1. Zr.gipaw.UPF O1 1. O.gipaw.UPF ATOMIC_POSITIONS Zr1 0.00000 0.00000 0.00000 Zr1 0.00000 0.50000 0.50000 Zr1 0.50000 0.00000 0.50000 Zr1 0.50000 0.50000 0.00000 O1 0.25000 0.25000 0.25000 O1 0.75000 0.75000 0.25000 O1 0.75000 0.25000 0.75000 O1 0.25000 0.75000 0.75000 O1 0.25000 0.25000 0.75000 O1 0.75000 0.75000 0.75000 O1 0.75000 0.25000 0.25000 K_POINTS {automatic} 2 2 2 0 0 0 ------------------------------------------------------------------ gipaw input file: &inputgipaw job = 'g_tensor' prefix = 'zro2' tmp_dir = './' isolve = 1 iverbosity = 1 q_gipaw = 0.01 ---------------------------------------------------------- pseudopotentials:Zr.gipaw.UPF ---------------------------------------------------------- < Generated using "atomic" code by A. Dal Corso (espresso distribution) Author: anonymous Generation date: 31Jul2008 Pseudopotential type: NC Element: Zr Functional: PBE Suggested minimum cutoff for wavefunctions: 65. Ry Suggested minimum cutoff for charge density: 259. Ry The Pseudo was generated with a Scalar-Relativistic Calculation L component and cutoff radius for Local Potential: 0 1.8000 Pseudopotential contains additional information for GIPAW reconstruction. Valence configuration: nl pn l occ Rcut Rcut US E pseu 4D 3 2 2.00 1.900 1.900 -0.287162 5S 1 0 2.00 3.785 3.785 -0.329274 Generation configuration: 5P 2 1 0.00 2.400 2.400 0.700000 4D 3 2 2.00 1.900 1.900 -0.264514 4D 3 2 0.00 1.900 1.900 -0.300000 5S 1 0 2.00 1.800 1.800 -0.326276 Pseudization used: rrkj .......... ------------------------------------------------------------------------- O.gipaw.UPF Generated using "atomic" code by A. Dal Corso (espresso distribution) Author: anonymous Generation date: 11Jul2007 O 0 The Pseudo was generated with a Non-Relativistic Calculation 1 1.4500000E+00 L component and cutoff radius for Local Potential nl pn l occ Rcut Rcut US E pseu 2S 1 0 2.00 1.45000000000 1.45000000000 -2.91141592981 2P 2 1 3.00 1.45000000000 1.45000000000 -1.79757641992 0 Version Number O Element NC Norm - Conserving pseudopotential F Nonlinear Core Correction SLA PW PBX PBC PBE Exchange-Correlation functional 6.00000000000 Z valence -30.28545848631 Total energy 0.000 0.000 Suggested cutoff for wfc and rho 1 Max angular momentum component 1095 Number of points in mesh 2 1 Number of Wavefunctions, Number of Projectors Wavefunctions nl l occ 2S 0 2.00 2P 1 3.00 ............. -------------------------------------------------------------------------------- Best regards, Yuan Wang School of Chemical Eng. & Techn., Tianjin Univ. E-mail: only1xiaoyuan at tju.edu.cn From bogus@does.not.exist.com Wed May 14 11:32:07 2008 From: bogus@does.not.exist.com () Date: Wed, 14 May 2008 09:32:07 -0000 Subject: No subject Message-ID: evaluated (integrated and converged) with respect to the same k-points. nscf (non-scf) only involves integrations of the special k-points using the charge density results from scf (which have been saved in the /tmp folder). No iteration is involved in nscf. Furthermore nscf obtains the mean value of the integration of wavefunctions when the k-points were sampled by Monkhorst-Pack method. Sometimes k-points are not so dense to integrate accurately (certain key points may be ignored). Compare with nscf, the fermi energy in scf should be mostly reasonable. When we want to calculation DOS we need to add more k-points for nscf and confirm that the identical fermi energies can be achieved. Otherwise we should trust the fermi energy from scf results when we deal with band structures and dos. Best regards, XQ Wang ===================================== X.Q. Wang wangxinquan at tju.edu.cn School of Chemical Engineering and Technology Tianjin University 92 Weijin Road, Tianjin, P. R. China tel:86-22-27890268, fax: 86-22-27892301 ===================================== --=====003_Dragon077838412722_===== Content-Type: text/html; charset="gb2312" Content-Transfer-Encoding: base64 PCFET0NUWVBFIEhUTUwgUFVCTElDICItLy9XM0MvL0RURCBIVE1MIDQuMCBUcmFuc2l0aW9uYWwv L0VOIj4NCjxIVE1MPjxIRUFEPg0KPE1FVEEgaHR0cC1lcXVpdj1Db250ZW50LVR5cGUgY29udGVu dD0idGV4dC9odG1sOyBjaGFyc2V0PUdCMjMxMiI+DQo8TUVUQSBjb250ZW50PSJNU0hUTUwgNi4w MC4yOTAwLjMzNTQiIG5hbWU9R0VORVJBVE9SPg0KPFNUWUxFPkBmb250LWZhY2Ugew0KCWZvbnQt ZmFtaWx5OiDLzszlOw0KfQ0KQGZvbnQtZmFjZSB7DQoJZm9udC1mYW1pbHk6IFZlcmRhbmE7DQp9 DQpAZm9udC1mYWNlIHsNCglmb250LWZhbWlseTogQMvOzOU7DQp9DQpAcGFnZSBTZWN0aW9uMSB7 c2l6ZTogNTk1LjNwdCA4NDEuOXB0OyBtYXJnaW46IDcyLjBwdCA5MC4wcHQgNzIuMHB0IDkwLjBw dDsgbGF5b3V0LWdyaWQ6IDE1LjZwdDsgfQ0KUC5Nc29Ob3JtYWwgew0KCVRFWFQtSlVTVElGWTog aW50ZXItaWRlb2dyYXBoOyBGT05ULVNJWkU6IDEwLjVwdDsgTUFSR0lOOiAwY20gMGNtIDBwdDsg Rk9OVC1GQU1JTFk6ICJUaW1lcyBOZXcgUm9tYW4iOyBURVhULUFMSUdOOiBqdXN0aWZ5DQp9DQpM 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