From gaoguoying at gmail.com Fri Dec 1 02:34:41 2006 From: gaoguoying at gmail.com (Guoying Gao) Date: Fri, 1 Dec 2006 09:34:41 +0800 Subject: [Pw_forum] questions on vc-relax Message-ID: <6234c0c60611301734n12474ee8w6446971be2c0bc9d@mail.gmail.com> Dear everyone, I am doing structure optimization and set "calculation=vc-relax", I'm confused that it doesn't converge no matter what I do. The following is what I have done: nstep=100, I tried dt with the values of 30,50,75,90,100,150 Also, I do the above things with different pseudopotentials, the results are still the same. I also read the truobleshooting in version of 3.2 of manual and Pw_forum, but I didn't find the suitable answers to my questions. The only prossible method is to increase variables "etot_conv_thr" and "forc_conv_thr", however, I don't know whether this will affect the accuracy of calculating the properties of the structure. Does anyone know the reason for this or the method to solve it? Thank you in advance! gao From akohlmey at cmm.chem.upenn.edu Fri Dec 1 03:06:51 2006 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Thu, 30 Nov 2006 21:06:51 -0500 (EST) Subject: [Pw_forum] questions on vc-relax In-Reply-To: <6234c0c60611301734n12474ee8w6446971be2c0bc9d@mail.gmail.com> Message-ID: On Fri, 1 Dec 2006, Guoying Gao wrote: dear gao, GG> Dear everyone, GG> I am doing structure optimization and set GG> "calculation=vc-relax", I'm confused that it doesn't converge no GG> matter what I do. The following is what I have done: what does not converge. the system size/shape, the atom positions, or the wavefunction? please provide some sample input or at least more details (atom types, atom count, plane wave cutoff). GG> nstep=100, I tried dt with the values of 30,50,75,90,100,150 GG> Also, I do the above things with different pseudopotentials, the GG> results are still the same. please provide a more detailed description of th 'symptoms'. GG> I also read the truobleshooting in version of 3.2 of manual and GG> Pw_forum, but I didn't find the suitable answers to my questions. The GG> only prossible method is to increase variables "etot_conv_thr" and GG> "forc_conv_thr", however, I don't know whether this will affect the GG> accuracy of calculating the properties of the structure. there have been multiple discussions on how to do this kind of calculation well, so please check the mailing list archives. first of all, you have to make sure that your stress tensor is reasonably converged with respect to the basis set, then you have to either use the 'constant cutoff'-scheme or raise the cutoff even further, so that you do not suffer from so-called pulay stress. rather tight convergence of the wavefunction is a requirement, too. it is probably best, you start experimenting with examples that are known to work, e.g. the ones presented at (with useful advice): http://www.vlab.msi.umn.edu/events/lecture.shtml GG> Does anyone know the reason for this or the method to solve it? since we don't know exactly, what your problem is, it is _very_ difficult to give any but very generic advice. whether this applies to your system or not, is very hard to tell. cheers, axel. GG> Thank you in advance! GG> GG> gao GG> _______________________________________________ GG> Pw_forum mailing list GG> Pw_forum at pwscf.org GG> http://www.democritos.it/mailman/listinfo/pw_forum GG> -- ======================================================================= 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 jin.zhang.pku at gmail.com Fri Dec 1 06:44:52 2006 From: jin.zhang.pku at gmail.com (Jin Zhang) Date: Fri, 1 Dec 2006 13:44:52 +0800 Subject: [Pw_forum] electron phonon interaction in ph.x In-Reply-To: <456F00F7.2050305@sissa.it> References: <5d233b6a0611300657r143c8acek65a0c4fdc6e40777@mail.gmail.com> <456F00F7.2050305@sissa.it> Message-ID: <5d233b6a0611302144u79ec7cc9keaafd5d4be4cf350@mail.gmail.com> I did a test in phonon.f90. The code is sth like this: USE ions_base, only : nat,amass complex(dp), allocatable :: work(:,:) allocate(work(3*nat,3*nat)) DO ipert = 1,3*nat DO jpert = 1,3*nat DO i=1,3*nat work(ipert,jpert) = work(ipert,jpert) + conjg(dyn(i,ipert))*amass(1)*dyn(i,jpert) ENDDO ENDDO ENDDO write(*,*) 'dynmat:' write(*,"(6(f12.8))") work(:,:) deallocate(work) ------------------------------------------ The output for example07 is: 1.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.00000000 0.00000000 The relation dyn^{\diag} * amass * dyn = I sustains indeed. Actually we're talking about the same thing. The inner product of eigenvector U^{\diag} M U gives scalar 1. While dyn^{\diag} * amass * dyn gives unit matrix. On 12/1/06, degironc wrote: > > Jin Zhang wrote: > > > 2. dyn(iat, jat): The dynamical matrix which obeys -- dyn^{\diag} * > > amass * dyn = 1 > > I don't think dymanical matric should obey this relation... > > EIGENVECTORS, U, of the generalized problem Dyn U = M U omega^2 will > obey > U^\dagger M U = 1 or something like that... > while > EIGENVECTORS, V=\sqrtM U of problem 1/sqrtM Dyn 1/sqrtM V = omega^2 V > will obey V^\dagger V = 1 > > stefano > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dep. of Physics, Peking University Beijing, P.R.China Phone: 86-10-62-753-190 -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061201/335a2ace/attachment.htm From degironc at sissa.it Fri Dec 1 09:09:22 2006 From: degironc at sissa.it (degironc) Date: Fri, 01 Dec 2006 09:09:22 +0100 Subject: [Pw_forum] electron phonon interaction in ph.x In-Reply-To: <5d233b6a0611302144u79ec7cc9keaafd5d4be4cf350@mail.gmail.com> References: <5d233b6a0611300657r143c8acek65a0c4fdc6e40777@mail.gmail.com> <456F00F7.2050305@sissa.it> <5d233b6a0611302144u79ec7cc9keaafd5d4be4cf350@mail.gmail.com> Message-ID: <456FE332.8040604@sissa.it> Dear Jin Zhang, we are probably saying the same thing... just notice that dyn(*,*) array after the call to routine dyndia IS NOT the dynamical matrix anymore but contains the eigenvectors... best, stefano Jin Zhang wrote: > I did a test in phonon.f90. The code is sth like this: > > USE ions_base, only : nat,amass > complex(dp), allocatable :: work(:,:) > allocate(work(3*nat,3*nat)) > > DO ipert = 1,3*nat > DO jpert = 1,3*nat > DO i=1,3*nat > work(ipert,jpert) = work(ipert,jpert) + > conjg(dyn(i,ipert))*amass(1)*dyn(i,jpert) > ENDDO > ENDDO > ENDDO > write(*,*) 'dynmat:' > write(*,"(6(f12.8))") work(:,:) > deallocate(work) > ------------------------------------------ > The output for example07 is: > 1.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 > 0.00000000 0.00000000 1.00000000 0.00000000 0.00000000 0.00000000 > 0.00000000 0.00000000 0.00000000 0.00000000 1.00000000 0.00000000 > The relation dyn^{\diag} * amass * dyn = I sustains indeed. > Actually we're talking about the same thing. The inner product of > eigenvector U^{\diag} M U gives scalar 1. > While dyn^{\diag} * amass * dyn gives unit matrix. > > On 12/1/06, *degironc* > > wrote: > > Jin Zhang wrote: > > > 2. dyn(iat, jat): The dynamical matrix which obeys -- dyn^{\diag} * > > amass * dyn = 1 > > I don't think dymanical matric should obey this relation... > > EIGENVECTORS, U, of the generalized problem Dyn U = M U > omega^2 will obey > U^\dagger M U = 1 or something like that... > while > EIGENVECTORS, V=\sqrtM U of problem 1/sqrtM Dyn 1/sqrtM V = omega^2 V > will obey V^\dagger V = 1 > > stefano > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > Dep. of Physics, Peking University > Beijing, P.R.China > Phone: 86-10-62-753-190 From rudrabnrj at gmail.com Fri Dec 1 13:22:30 2006 From: rudrabnrj at gmail.com (rudra Banerjee) Date: Fri, 1 Dec 2006 17:52:30 +0530 Subject: [Pw_forum] smearing methods and relaxation In-Reply-To: <456EF9AA.2010808@mit.edu> References: <9d7293e10611300721p1d8d35b6tffa3dd8b28b58acb@mail.gmail.com> <456EF9AA.2010808@mit.edu> Message-ID: <2e36f8e50612010422i6acc8226s915c4a05d04cb47a@mail.gmail.com> hello friend can you name a good resource on knowing what smearing is? On 11/30/06, Nicola Marzari wrote: > > > > > Hi Jess, you should use a smearing instead (usually methfessel-paxton or > marzari-vanderbilt). You need to use a small value - try 0.4 eV > (remember, pwscf uses Ry, so divide by 13.6), and make sure > that whatever you want to calculate is converged with respect > to k-points. > > 0.4eV might be too large for a lot of critical properties - so decrease > it (and increase, by a lot, the kpoints) and see if things change. > > nicola > > > Jess Kondor wrote: > > > > Hello, everyone, > > > > I have a question about smearing methods and relaxation, in > > particularly tetrahedron method and structural optimization in case of > > metals. VASP manual recommends do not use tetrahedron method in > > relaxation of metals because this method is not variational with respect > > to the partial occupancies, which means, that the calculated forces are > > wrong by 5 to 10 % in metals. Is it applicable in pwscf case? I am > > studying magnetic system (which is metal without U correction, and > > should be insulator with LSDA+U) and I am not sure it is good idea to > > use 'tetrahedra' in this case. What do you suggest? > > > > Regards, > > > > JK > > > -- > --------------------------------------------------------------------- > 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 > -- rudra ------------------------- have a good time! -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061201/e741424c/attachment.htm From degironc at sissa.it Fri Dec 1 13:28:25 2006 From: degironc at sissa.it (degironc) Date: Fri, 01 Dec 2006 13:28:25 +0100 Subject: [Pw_forum] smearing methods and relaxation In-Reply-To: <2e36f8e50612010422i6acc8226s915c4a05d04cb47a@mail.gmail.com> References: <9d7293e10611300721p1d8d35b6tffa3dd8b28b58acb@mail.gmail.com> <456EF9AA.2010808@mit.edu> <2e36f8e50612010422i6acc8226s915c4a05d04cb47a@mail.gmail.com> Message-ID: <45701FE9.1070908@sissa.it> dear rudra Banerjee, if you happen by any chance to have a look inside INPUT_PW where the variable smearing is defined you'll find a couple of references. hope this help. stefano rudra Banerjee wrote: > hello friend > can you name a good resource on knowing what smearing is? > > On 11/30/06, *Nicola Marzari* > wrote: > > > > > Hi Jess, you should use a smearing instead (usually > methfessel-paxton or > marzari-vanderbilt). You need to use a small value - try 0.4 eV > (remember, pwscf uses Ry, so divide by 13.6), and make sure > that whatever you want to calculate is converged with respect > to k-points. > > 0.4eV might be too large for a lot of critical properties - so > decrease > it (and increase, by a lot, the kpoints) and see if things change. > > nicola > > > Jess Kondor wrote: > > > > Hello, everyone, > > > > I have a question about smearing methods and relaxation, in > > particularly tetrahedron method and structural optimization in > case of > > metals. VASP manual recommends do not use tetrahedron method in > > relaxation of metals because this method is not variational with > respect > > to the partial occupancies, which means, that the calculated > forces are > > wrong by 5 to 10 % in metals. Is it applicable in pwscf case? I am > > studying magnetic system (which is metal without U correction, and > > should be insulator with LSDA+U) and I am not sure it is good > idea to > > use 'tetrahedra' in this case. What do you suggest? > > > > Regards, > > > > JK > > > -- > --------------------------------------------------------------------- > 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 > > > > > -- > rudra > ------------------------- > have a good time! From cesards at msi.umn.edu Fri Dec 1 16:02:08 2006 From: cesards at msi.umn.edu (cesards at msi.umn.edu) Date: Fri, 1 Dec 2006 09:02:08 -0600 (CST) Subject: [Pw_forum] Re: questions on vc-relax (Guoying Gao) Message-ID: <49338.201.6.62.182.1164985328.squirrel@www.msi.umn.edu> Dear Gao, You have provided little information, so I can only guess what could be wrong. Before submiting the question again, try this: 1) Set a small value for conv_thr, like 1.0d-8. At least 3 or 4 orders of magnitude smaller than etot_conv_thr. 2) Check the value You set to wmass in &CELL namelist. It will depend on the atomic masses, wmass = 0.003 is typical for a 64 atoms cell with all atomic masses set to 20.0. Try variations within one order of magnitude. 3) Set all atomic masses to the same value for faster convergence. Cesar. From jzwanzig at dal.ca Fri Dec 1 13:52:59 2006 From: jzwanzig at dal.ca (Josef Zwanziger) Date: Fri, 01 Dec 2006 08:52:59 -0400 Subject: [Pw_forum] Some efg.x confusions cleared up Message-ID: <1164977579.7276.18.camel@jzwanzig-laptop> Dear Colleagues-- last month I posted some questions and concerns about the efg.x code. Here's an update--first, concerning units of the quadrupole moment, I found that the expressions in efg.x are correct after all, provided that you interpret the input unit as 10E-30 m^2 (the documentation is a little unclear on this, but no matter). Therefore, for oxygen-17 the correct input is 2.58, as example24 uses. I was able to trace the issue back to faulty data published on www.webelements.com, where there is in fact a confusion about the definition of the unit of barns (a little disturbing, as this is probably the best known web site for beginning chemistry students to assemble data). Second, concerning the pseudopotentials used in example24, I was finally able to reconstruct the appropriate input files for oxygen, following those for silicon in atomic_doc/pseudo-gen, so that using ld1.x I can make both Si, O, and .recon files that reproduce the example24 data. However, life is quite simple yet--if I change the pseudopotentials in any way, say by using lloc=2 instead of lloc=1, or using 2 projectors in each channel, the computed Cq's for oxygen in SiO2 change by orders of magnitude. I'm still trying to understand why this works this way. Best, Joe Zwanziger Josef W. Zwanziger Prof. of Chemistry Canada Research Chair in NMR Studies of Materials Director, Atlantic Region Magnetic Resonance Centre Dalhousie University Halifax, NS B3H 4J3=20 Canada tel: 902.494.1960 net: jzwanzig at dal.ca fax: 902.494.1867 web: http://jwz.chem.dal.ca From hqzhou at nju.edu.cn Sat Dec 2 09:38:33 2006 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Sat, 2 Dec 2006 16:38:33 +0800 Subject: [Pw_forum] use doual core References: <7b6913e90611220734s15038d2ei36e1e7a28166f146@mail.gmail.com> <002e01c71207$5e733cb0$1d00a8c0@solarflare> Message-ID: <005f01c715ed$4104e220$1d00a8c0@solarflare> Amin, Sorry, I was out of the town and had no access to my e-mail. 1. You can use anyone of MPI implemetations. But I recommend Intel MPI-2 because it's an installable binary, it saves you as a beginner a lot of time. If you cannot get a copy of that, use OpenMPI, a successor of LAM/MPI. 2. Basically, when you recompile MPI, you can add --prefix=/your/favourite/place to configure 3. You need C compiler to compile MPI. You need gcc too. I compiled MPI with icc + ifort. Good luck! Huiqun ----- Original Message ----- From: Amin Babazadeh To: pw_forum at pwscf.org Sent: Thursday, November 30, 2006 3:17 PM Subject: Re: [Pw_forum] use doual core Thanks a lot for your answers.but until yet i couldn't solve my problem.I confused about mpi. there are three kind of mpi in the Internet (lam/mpi,openmpi,mpich) i don't know which one of them i should install. about making the environment i should say that i am beginner in using Linux so i use the ./configure commend and i didn't change any path because i don't know how i should do it. i will appreciate if answer my question? 1-which mpi do i need for my job? 2-how could i change the path? 3-is ifort compiler enough for installing mpi package? Thanks a lot On 11/27/06, Huiqun Zhou wrote: ? Have you set up you environment for using one the mpi libraries you installed in .bashrc? For example, for openmpi you need to set following in your .bashrc if you are using bash as your shell: ... export PATH=/opt/openmpi/bin:$PATH export LD_LIBRARY_PATH=/opt/openmpi/lib:$LD_LIBRARY_PATH ... Note: you need to replace /opt/openmpi with the path of your installation. Huiqun Zhou ----- Original Message ----- From: Amin Babazadeh To: pw_forum at pwscf.org Sent: Sunday, November 26, 2006 6:11 PM Subject: Re: [Pw_forum] use doual core Dear Dr.Kohlmeyer Thanks a lot for your help.I did what you said.i installed fftw-3.1.2.tar lam-7.1.2.tar mpich2-1.0.4p1.tar openmpi-1.1.2.tar on fedora core 5 and after that i configure the espresso but this error was written WARNING: the following problems were detected: unsupported C/Fortran compilers combination: CC=mpicc, F77=mpif77, F90=mpif90 you may not be able to compile this program. i don't know what this problem means.would you please help me. Thanks a lot On 11/22/06, Axel Kohlmeyer wrote: On 11/22/06, Amin Babazadeh < babazade at gmail.com> wrote: > dear users > I use a computer with a dual core CPU.but my problem is that when i run a > program only one of the CPU work but i like to share the work (solving k > points) between cpus. > I think that i should install the parallel pwscf but when i run the > ./configure only single pwscf installed. you have to install an MPI package (e.g. LAM/MPI, OpenMPI, MPICH) first and then configure/compile quantum espresso with parallel support as explained in the provided installation instructions. please make sure that your MPI package is compatible with or compiled for the fortran compiler you want to use to compiled quantum espresso with. precompiled packages may be compiled for a different compiler and thus need special flags or environment variables set to use the compiler of your choice. axel. > would you please tell me or give me a document that solve my problem. > > > -- > AMIN -- ======================================================================= 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 -- AMIN -- AMIN -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061202/0afdc5ee/attachment.htm From babazade at gmail.com Sat Dec 2 14:19:41 2006 From: babazade at gmail.com (Amin Babazadeh) Date: Sat, 2 Dec 2006 16:49:41 +0330 Subject: [Pw_forum] use doual core In-Reply-To: <005f01c715ed$4104e220$1d00a8c0@solarflare> References: <7b6913e90611220734s15038d2ei36e1e7a28166f146@mail.gmail.com> <002e01c71207$5e733cb0$1d00a8c0@solarflare> <005f01c715ed$4104e220$1d00a8c0@solarflare> Message-ID: Dear Dr.Zhou and kohlmeyer Thanks a lot for your helps. i will try to do your recommendation. Sincerely yours amin On 12/2/06, Huiqun Zhou wrote: > > Amin, > > Sorry, I was out of the town and had no access to my e-mail. > > 1. You can use anyone of MPI implemetations. But I recommend Intel MPI-2 > because it's an > installable binary, it saves you as a beginner a lot of time. If you > cannot get a copy of that, > use OpenMPI, a successor of LAM/MPI. > 2. Basically, when you recompile MPI, you can add > --prefix=/your/favourite/place to configure > 3. You need C compiler to compile MPI. You need gcc too. I compiled MPI > with icc + ifort. > > Good luck! > > Huiqun > > > ----- Original Message ----- > *From:* Amin Babazadeh > *To:* pw_forum at pwscf.org > *Sent:* Thursday, November 30, 2006 3:17 PM > *Subject:* Re: [Pw_forum] use doual core > > Thanks a lot for your answers.but until yet i couldn't solve my problem.Iconfused about mpi. there are three kind of mpi in the Internet > (lam/mpi,openmpi,mpich) i don't know which one of them i should install. > about making the environment i should say that i am beginner in using > Linux so i use the ./configure commend and i didn't change any path because > i don't know how i should do it. > i will appreciate if answer my question? > 1-which mpi do i need for my job? > 2-how could i change the path? > 3-is ifort compiler enough for installing mpi package? > Thanks a lot > > On 11/27/06, Huiqun Zhou wrote: > > > > Have you set up you environment for using one the mpi libraries you > > installed in .bashrc? > > For example, for openmpi you need to set following in your .bashrc if > > you are using bash > > as your shell: > > ... > > export PATH=/opt/openmpi/bin:$PATH > > export LD_LIBRARY_PATH=/opt/openmpi/lib:$LD_LIBRARY_PATH > > ... > > > > Note: you need to replace /opt/openmpi with the path of your > > installation. > > > > Huiqun Zhou > > > > > > ----- Original Message ----- > > *From:* Amin Babazadeh > > *To:* pw_forum at pwscf.org > > *Sent:* Sunday, November 26, 2006 6:11 PM > > *Subject:* Re: [Pw_forum] use doual core > > > > > > Dear Dr.Kohlmeyer > > Thanks a lot for your help.I did what you said.i installed > > fftw-3.1.2.tar > > lam-7.1.2.tar > > mpich2-1.0.4p1.tar > > openmpi-1.1.2.tar > > on fedora core 5 and after that i configure the espresso but this error > > was written > > > > WARNING: the following problems were detected: > > > > unsupported C/Fortran compilers combination: > > CC=mpicc, F77=mpif77, F90=mpif90 > > you may not be able to compile this program. > > i don't know what this problem means.would you please help me. > > Thanks a lot > > > > > > > > On 11/22/06, Axel Kohlmeyer wrote: > > > > > > On 11/22/06, Amin Babazadeh < babazade at gmail.com> wrote: > > > > dear users > > > > I use a computer with a dual core CPU.but my problem is that when i > > > run a > > > > program only one of the CPU work but i like to share the work > > > (solving k > > > > points) between cpus. > > > > I think that i should install the parallel pwscf but when i run the > > > > ./configure only single pwscf installed. > > > > > > you have to install an MPI package (e.g. LAM/MPI, OpenMPI, MPICH) > > > first and then configure/compile quantum espresso with parallel > > > support > > > as explained in the provided installation instructions. > > > > > > please make sure that your MPI package is compatible with or compiled > > > for the fortran compiler you want to use to compiled quantum espresso > > > with. > > > precompiled packages may be compiled for a different compiler and thus > > > > > > need special flags or environment variables set to use the compiler of > > > your choice. > > > > > > axel. > > > > > > > would you please tell me or give me a document that solve my > > > problem. > > > > > > > > > > > > -- > > > > AMIN > > > > > > > > > -- > > > > > > ======================================================================= > > > 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 > > > > > > > > > > > -- > > AMIN > > > > > > > -- > AMIN > > -- AMIN -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061202/db26f6a0/attachment.htm From ongphuongvu at yahoo.com Sun Dec 3 05:36:53 2006 From: ongphuongvu at yahoo.com (vu ongphuong) Date: Sat, 2 Dec 2006 20:36:53 -0800 (PST) Subject: [Pw_forum] Electron-phonon interaction in insulators Message-ID: <942614.7069.qm@web50613.mail.yahoo.com> Dear all users, As what I know, there exist the electron-phonon interaction in insulators. My question is: Can PWSCF calculate the electron-phonon interaction in in insulators? Thank you in advance --------------------------------- Everyone is raving about the all-new Yahoo! Mail beta. -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061202/e49ccf55/attachment.htm From gaoguoying at gmail.com Sun Dec 3 07:44:56 2006 From: gaoguoying at gmail.com (Guoying Gao) Date: Sun, 3 Dec 2006 14:44:56 +0800 Subject: [Pw_forum] questions on vc-relax In-Reply-To: <6234c0c60612010214r3ee59aa8o480e3b73c93772f9@mail.gmail.com> References: <6234c0c60611301734n12474ee8w6446971be2c0bc9d@mail.gmail.com> <6234c0c60612010214r3ee59aa8o480e3b73c93772f9@mail.gmail.com> Message-ID: <6234c0c60612022244s7ff992d8g9afc3d0950437c4f@mail.gmail.com> Dear Axel, I'm sorry for my ambiguous esperssions. I mean that in the process of relaxing, either "etot_conv_thr" or "forc_con_thr" ( or both ) does not converge. I have attached my input and output files(in the accessory). Another question: >>first of all, you have to make sure that your stress tensor is >>reasonably converged with respect to the basis set How to judge that stress tensor converges with respect to the basis set. The following is my input files: &control calculation='vc-relax', restart_mode='from_scratch', dt=30, prefix='n2', pseudo_dir = '/home/cpmd/yanming/ggy/pseudo/', outdir='/home/cpmd/yanming/ggy/tmp/tmp0/', tstress=.t., tprnfor=.t., nstep= 100 / &system ibrav= 8, celldm(1) =7.85937,celldm(2)=0.66482327482567924981, celldm(3)=1.21158932435681654243, nat= 8, ntyp= 1,ecutwfc =30, ecutrho=300, nosym = .t. / &electrons mixing_beta = 0.7 conv_thr = 1.0d-8 / &IONS ion_dynamics = 'damp' upscale = 20 / &CELL cell_dynamics = 'damp-pr' press =800 / ATOMIC_SPECIES N 14.0067 N.pbe-van_ak.UPF ATOMIC_POSITIONS {crystal} N 0.39750000 0.86660000 0.19890000 N 0.92010000 0.64090000 0.05920000 N 0.60250000 0.13340000 0.69890000 N 0.07990000 0.35910000 0.55920000 N 0.60250000 0.86660000 0.30110000 N 0.07990000 0.64090000 0.44080000 N 0.39750000 0.13340000 0.80110000 N 0.92010000 0.35910000 -0.05920000 K_POINTS { automatic } 5 8 4 0 0 0 Thank you again! gao From hqzhou at nju.edu.cn Sun Dec 3 09:49:49 2006 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Sun, 3 Dec 2006 16:49:49 +0800 Subject: [Pw_forum] questions on vc-relax References: <6234c0c60611301734n12474ee8w6446971be2c0bc9d@mail.gmail.com> <6234c0c60612010214r3ee59aa8o480e3b73c93772f9@mail.gmail.com> <6234c0c60612022244s7ff992d8g9afc3d0950437c4f@mail.gmail.com> Message-ID: <004401c716b7$fe6e82b0$1d00a8c0@solarflare> You can firstly try to reduce mixing_beta to 0.1 or smaller. Huiqun Zhou ----- Original Message ----- From: "Guoying Gao" To: Sent: Sunday, December 03, 2006 2:44 PM Subject: Re: [Pw_forum] questions on vc-relax > Dear Axel, > I'm sorry for my ambiguous esperssions. I mean that in the process > of relaxing, either "etot_conv_thr" or "forc_con_thr" ( or both ) > does not converge. I have attached my input and output files(in the > accessory). > > Another question: > >>first of all, you have to make sure that your stress tensor is > >>reasonably converged with respect to the basis set > How to judge that stress tensor converges with respect to the basis set. > > > The following is my input files: > > &control > calculation='vc-relax', > restart_mode='from_scratch', > dt=30, > prefix='n2', > pseudo_dir = '/home/cpmd/yanming/ggy/pseudo/', > outdir='/home/cpmd/yanming/ggy/tmp/tmp0/', > tstress=.t., > tprnfor=.t., > nstep= 100 > / > &system > ibrav= 8, celldm(1) =7.85937,celldm(2)=0.66482327482567924981, > celldm(3)=1.21158932435681654243, > nat= 8, ntyp= 1,ecutwfc =30, ecutrho=300, nosym = .t. > / > &electrons > mixing_beta = 0.7 > conv_thr = 1.0d-8 > / > &IONS > ion_dynamics = 'damp' > upscale = 20 > / > &CELL > cell_dynamics = 'damp-pr' > press =800 > / > ATOMIC_SPECIES > N 14.0067 N.pbe-van_ak.UPF > ATOMIC_POSITIONS {crystal} > N 0.39750000 0.86660000 0.19890000 > N 0.92010000 0.64090000 0.05920000 > N 0.60250000 0.13340000 0.69890000 > N 0.07990000 0.35910000 0.55920000 > N 0.60250000 0.86660000 0.30110000 > N 0.07990000 0.64090000 0.44080000 > N 0.39750000 0.13340000 0.80110000 > N 0.92010000 0.35910000 -0.05920000 > K_POINTS { automatic } > 5 8 4 0 0 0 > > Thank you again! > gao > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From shuixblue at hotmail.com Sun Dec 3 09:50:32 2006 From: shuixblue at hotmail.com (guo shuix) Date: Sun, 03 Dec 2006 16:50:32 +0800 Subject: [Pw_forum] how to get the results of atomic dipole and quadrupole moment Message-ID: Dear all: Does anyone can shed light on me how to get the results of atomic dipole and quadrupole moment(the direction pointing outwards of the surface) when adatom adsorption on the nonpolar-slab surface(one-side model) using pwscf? I searched out some relative information in maillist, but few can help me solve the problem. Much guidance and direction is deeply appreciated. Best regards! shuix _________________________________________________________________ ?????????????? MSN Messenger: http://messenger.msn.com/cn From jin.zhang.pku at gmail.com Sun Dec 3 12:23:59 2006 From: jin.zhang.pku at gmail.com (Jin Zhang) Date: Sun, 3 Dec 2006 19:23:59 +0800 Subject: [Pw_forum] Electron-phonon interaction in insulators In-Reply-To: <942614.7069.qm@web50613.mail.yahoo.com> References: <942614.7069.qm@web50613.mail.yahoo.com> Message-ID: <5d233b6a0612030323w50c3451ckcde0b4b9dece6ccd@mail.gmail.com> I have tested this in an isolated H2 molecule by setting occ to smearing, though this kind of calculation doesn't make much sense. Regards, Jin Zhang On 12/3/06, vu ongphuong wrote: > > Dear all users, > > As what I know, there exist the electron-phonon interaction in insulators. > My question is: > > Can PWSCF calculate the electron-phonon interaction in in insulators? > > Thank you in advance > > > > > ------------------------------ > Everyone is raving about the all-new Yahoo! Mail beta. > > -- Dep. of Physics, Peking University Beijing, P.R.China Phone: 86-10-62-753-190 -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061203/829d6142/attachment.htm From marzari at MIT.EDU Sun Dec 3 18:11:20 2006 From: marzari at MIT.EDU (Nicola Marzari) Date: Sun, 03 Dec 2006 12:11:20 -0500 Subject: [Pw_forum] how to get the results of atomic dipole and quadrupole moment In-Reply-To: References: Message-ID: <45730538.2040907@mit.edu> You have a few possibilities - all require some coding or gaining more expertise on the codes. I would also guess that this issue has been discussed in the '90s - e.g. in papers from the group of Matthias Scheffler in Berlin. First of all, you need to realize that there is no unique or physical definition of an atomic multipole when the atom is not isolated, but adsorbed - you can only 1) discuss the electrostatic of the global system, or 2) you need to partition the charge density. This latter can only be done heuristically, e.g. using Wannier functions. 1) The first possibility would be to calculate the e.g. dipole for the clean slab, and the dipole for slab with the adatom. Then, you have the difference in dipoles induced by the presence of the adatom. The code gives you the charge density on a grid, so you are all set. Alternatively, you can look at the charge density difference between the adatom with the slab, minus the clean slab, minus the isolated atom, and calculate the multipoles of this charge distribution. You also need to think about which coordinates to use for the clean slab - those of the relaxed slab with the adatom adsorbed, or the relaxed clean slab. 2) If you want a more "local" descriptor, you could try calculating the maximally-localized Wannier functions for your system - then the centers of these give you a classical electrostatic representation of the electrons, and you could use them (or, even better, the charge distribution form the Wannier functions themselves) to heuristically define the dipole or quadrupole of the adsorbed atom. nicola PS: as always - if you can, do sign with a full name and affiliation. I would like to know who uses the codes, and where, and this information is EXTREMELY helpful to all the developers. guo shuix wrote: > Dear all: > Does anyone can shed light on me how to get the results of atomic > dipole and quadrupole moment(the direction pointing outwards of the > surface) when adatom adsorption on the nonpolar-slab surface(one-side > model) using pwscf? I searched out some relative information in > maillist, but few can help me solve the problem. Much guidance and > direction is deeply appreciated. > Best regards! > > shuix > > _________________________________________________________________ > ?????????????? MSN Messenger: http://messenger.msn.com/cn > _______________________________________________ > 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 gaoguoying at gmail.com Mon Dec 4 04:06:41 2006 From: gaoguoying at gmail.com (Guoying Gao) Date: Mon, 4 Dec 2006 11:06:41 +0800 Subject: [Pw_forum] questions on vc-relax In-Reply-To: <004401c716b7$fe6e82b0$1d00a8c0@solarflare> References: <6234c0c60611301734n12474ee8w6446971be2c0bc9d@mail.gmail.com> <6234c0c60612010214r3ee59aa8o480e3b73c93772f9@mail.gmail.com> <6234c0c60612022244s7ff992d8g9afc3d0950437c4f@mail.gmail.com> <004401c716b7$fe6e82b0$1d00a8c0@solarflare> Message-ID: <6234c0c60612031906m185e9587q3397b2f131dd1a28@mail.gmail.com> Hi Zhou, I tried seting mixing_beta to 0.1, but it doesn't work yet.The convergence of etot_conv_thr and forc_conv_thr are still not achieved. Thank you all the same. Gao From lvtieyu1975 at yahoo.com.cn Mon Dec 4 06:27:47 2006 From: lvtieyu1975 at yahoo.com.cn (=?gb2312?q?=BB=AA=20=C0=EE?=) Date: Mon, 4 Dec 2006 13:27:47 +0800 (CST) Subject: [Pw_forum] GW approximation Message-ID: <304992.55382.qm@web15806.mail.cnb.yahoo.com> Dear all: I'm interesting in GW approximation. I find that the code has inferface for GWA. Can the code run GWA? Or which GWA code can read the result of PWscf? Best wish Tieyu Lu --------------------------------- Mp3???-??????? -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061204/ce9de9e1/attachment.htm From lanhaiping at gmail.com Mon Dec 4 07:53:25 2006 From: lanhaiping at gmail.com (lan haiping) Date: Mon, 4 Dec 2006 14:53:25 +0800 Subject: [Pw_forum] GW approximation In-Reply-To: <304992.55382.qm@web15806.mail.cnb.yahoo.com> References: <304992.55382.qm@web15806.mail.cnb.yahoo.com> Message-ID: Hi, To my knowledge, Pwscf can do gw calculation with interface to SELF code, which does not publically obtain yet .. On 12/4/06, ? ? wrote: > > Dear all: > > I'm interesting in GW approximation. I find that the code has inferface > for GWA. Can the code run GWA? Or which GWA code can read the result of > PWscf? > > Best wish > > Tieyu Lu > > ------------------------------ > Mp3???-??????? > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061204/f7956a54/attachment.htm From yuwen_66 at yahoo.com Mon Dec 4 07:57:41 2006 From: yuwen_66 at yahoo.com (W. YU) Date: Sun, 3 Dec 2006 22:57:41 -0800 (PST) Subject: [Pw_forum] symmetry selection in CELL_PARAMETERS Message-ID: <20061204065741.72556.qmail@web51004.mail.yahoo.com> Dear pw users, I have two questions which I hope someone might help me. 1. I tried to do a antiferromegnetic calculation. I know it is an insolator with a small gap, but for such a calcultion, I have to add smearing to change the occupancy of the elcetrons in order for the code to work. Am I doing it right or there is an alternative ? 2. I tested calcualting the elastic constants using stain-energy method with pwscf. I set the ibrav=0 and privided the additional card CELL_PARAMETERS. But there is a symmetry selection for this card. Either CUBIC or HEXGONAL. I know the symmetry before applying the strain (say cubic). My question is: is it possible that the strained lattice changes its symmetry from cubic to hexgonal or vice versa? If this does happen, if I still use the same symmetry as the unstrained lattice, will this effect the calcualtion results? Thanks a lot W. YU ____________________________________________________________________________________ Any questions? Get answers on any topic at www.Answers.yahoo.com. Try it now. From lanhaiping at gmail.com Mon Dec 4 10:32:12 2006 From: lanhaiping at gmail.com (lan haiping) Date: Mon, 4 Dec 2006 17:32:12 +0800 Subject: [Pw_forum] compilation error for CPV 3.2 Message-ID: Hi, I have come to error when i compiled new version of espresso 3.2. My computer is X86-64, Redhat with pgi 6.0 compilor and acml mathlib. There is no such problem when compiling order version. Would you please give me some hints or suggestion ? The error information is below: " *mpif90 -fast -r8 -D__PGI -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA -I../include -I./ -I../Mo dules -I../iotk/src -I../PW -I../PH -I../CPV -c wave.F90 -o wave.o Lowering Error: nonconstant multiplier for dimension 1 for datatype 6 PGF90-F-0000-Internal compiler error. Errors in Lowering 1 (wave.F90: 69) PGF90/any Linux/x86-64 6.0-5: compilation aborted make[1]: *** [wave.o] Error 2 make[1]: Leaving directory `/home/haiping/espresso-3.2/CPV' make: *** [cp] Error 2 * " -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061204/339063bf/attachment.htm From giannozz at nest.sns.it Mon Dec 4 11:32:25 2006 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 4 Dec 2006 11:32:25 +0100 Subject: [Pw_forum] symmetry selection in CELL_PARAMETERS In-Reply-To: <20061204065741.72556.qmail@web51004.mail.yahoo.com> References: <20061204065741.72556.qmail@web51004.mail.yahoo.com> Message-ID: <5287BE93-1456-450B-87EB-583E642D9608@nest.sns.it> On Dec 4, 2006, at 7:57 , W. YU wrote: > 1. I tried to do a antiferromegnetic calculation. I know it is an > insulator > with a small gap, but for such a calcultion, I have to add smearing > to change the occupancy of the electrons in order for the code to > work. > Am I doing it right or there is an alternative ? there are many alternatives, but smearing works for both metals and insulators, if properly chosen (i.e. small for insulators) > 2. I tested calculating the elastic constants using stain-energy > method > with pwscf. I set the ibrav=0 and provided the additional card > CELL_PARAMETERS. But there is a symmetry selection for this card. > Either CUBIC or HEXGONAL. I know the symmetry before applying the > strain (say cubic). then there is no problem: after applying a strain, the symmetry group will be a subgroup of the unstrained symmetry group Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at nest.sns.it Mon Dec 4 11:46:52 2006 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 4 Dec 2006 11:46:52 +0100 Subject: [Pw_forum] compilation error for CPV 3.2 In-Reply-To: References: Message-ID: <82842437-979B-4820-8140-D2635E8753FF@nest.sns.it> On Dec 4, 2006, at 10:32 , lan haiping wrote: > I have come to error when i compiled new version of espresso 3.2. > My computer is X86-64, Redhat with pgi 6.0 compilor and acml > mathlib. There is no such problem when compiling order version. > Would you please give me some hints or suggestion ? as explained no less than 1001 times, "Internal compiler error" means, by definition, that there is a bug in the compiler. Since PGI costs a lot of money, you should complain with PGI. Standard suggestions in the users' guide include - lowering optimization level - installing all available patches - trying to figure out which part of the code triggers the bug and trying to modifying it - using a different compiler that works on the architecture of your machine (such as for instance Intel or g95) Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From hqzhou at nju.edu.cn Mon Dec 4 12:15:19 2006 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Mon, 4 Dec 2006 19:15:19 +0800 Subject: [Pw_forum] questions on vc-relax References: <6234c0c60611301734n12474ee8w6446971be2c0bc9d@mail.gmail.com> <6234c0c60612010214r3ee59aa8o480e3b73c93772f9@mail.gmail.com> <6234c0c60612022244s7ff992d8g9afc3d0950437c4f@mail.gmail.com> <004401c716b7$fe6e82b0$1d00a8c0@solarflare> <6234c0c60612031906m185e9587q3397b2f131dd1a28@mail.gmail.com> Message-ID: <00c201c71795$7b8506b0$1d00a8c0@solarflare> Gao, I think you really had better to give us more description about you trouble. I did very little changes to your input (nosym and upscale) and I don't think these changes are crucial, your case is now running on my cluster parallelly (4 cpu on one node). By far, the calculation is normal although not finished, total force has been reduced to 0.0x, pressure already stable around 800 kbar ... Hope you have figured out the problem. Huiqun ----- Original Message ----- From: "Guoying Gao" To: Sent: Monday, December 04, 2006 11:06 AM Subject: Re: [Pw_forum] questions on vc-relax > Hi Zhou, > I tried seting mixing_beta to 0.1, but it doesn't work yet.The > convergence of etot_conv_thr and forc_conv_thr are still not achieved. > Thank you all the same. > Gao > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From hqzhou at nju.edu.cn Tue Dec 5 04:51:43 2006 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Tue, 5 Dec 2006 11:51:43 +0800 Subject: [Pw_forum] questions on vc-relax References: <6234c0c60611301734n12474ee8w6446971be2c0bc9d@mail.gmail.com> <6234c0c60612010214r3ee59aa8o480e3b73c93772f9@mail.gmail.com> <6234c0c60612022244s7ff992d8g9afc3d0950437c4f@mail.gmail.com> <004401c716b7$fe6e82b0$1d00a8c0@solarflare> <6234c0c60612031906m185e9587q3397b2f131dd1a28@mail.gmail.com> Message-ID: <005001c71820$ae2ccc20$1d00a8c0@solarflare> Gao, Here are the final results of your case. It costed 1h48m wall time to finish on a machine with 2 dual core dempsey 3.0GHz CPUs. Numerically, it has been converged. But you need to check if you have got physics you expected, phase transition, so on. This is what I can't help you;-) Usually, vc-relax takes long time to converge, the higher the applied pressure is, the longer of time it'll take. So, be patient. Huiqun ...... ! total energy = -158.31956954 Ry Harris-Foulkes estimate = -158.31956955 Ry estimated scf accuracy < 2.5E-09 Ry convergence has been achieved Forces acting on atoms (Ry/au): atom 1 type 1 force = 0.00014512 0.00003251 -0.00031974 atom 2 type 1 force = 0.00002286 -0.00003062 -0.00002411 atom 3 type 1 force = -0.00014512 -0.00003251 -0.00031974 atom 4 type 1 force = -0.00002286 0.00003062 -0.00002411 atom 5 type 1 force = -0.00014512 0.00003251 0.00031974 atom 6 type 1 force = -0.00002286 -0.00003062 0.00002411 atom 7 type 1 force = 0.00014512 -0.00003251 0.00031974 atom 8 type 1 force = 0.00002286 0.00003062 0.00002411 Total force = 0.000711 Total SCF correction = 0.000098 entering subroutine stress ... total stress (Ry/bohr**3) (kbar) P= 799.98 0.00543548 0.00000000 0.00000000 799.59 0.00 0.00 0.00000000 0.00543736 0.00000000 0.00 799.86 0.00 0.00000000 0.00000000 0.00544167 0.00 0.00 800.50 Parrinello-Rahman Damped Dynamics: convergence achieved, final= -158.31956954 ------------------------------------------------------------------------ Final estimate of lattice vectors (input alat units) 0.967475312 0.000000000 0.000000000 0.000000000 0.633927072 0.000000000 0.000000000 0.000000000 1.338665770 final unit-cell volume = 398.5791 (a.u.)^3 input alat = 7.8594 (a.u.) CELL_PARAMETERS (alat) 0.967475312 0.000000000 0.000000000 0.000000000 0.633927072 0.000000000 0.000000000 0.000000000 1.338665770 ATOMIC_POSITIONS (crystal) N 0.395192734 1.136368579 0.186833743 N 0.924219436 0.647523089 0.069267896 N 0.604807266 -0.136368579 0.686833743 N 0.075780564 0.352476911 0.569267896 N 0.604807266 1.136368579 0.313166257 N 0.075780564 0.647523089 0.430732104 N 0.395192734 -0.136368579 0.813166257 N 0.924219436 0.352476911 -0.069267896 Writing output data file n2.save PWSCF : 1h14m CPU time, 1h48m wall time ----- Original Message ----- From: "Guoying Gao" To: Sent: Monday, December 04, 2006 11:06 AM Subject: Re: [Pw_forum] questions on vc-relax > Hi Zhou, > I tried seting mixing_beta to 0.1, but it doesn't work yet.The > convergence of etot_conv_thr and forc_conv_thr are still not achieved. > Thank you all the same. > Gao > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From fengjie.ma at gmail.com Tue Dec 5 05:34:10 2006 From: fengjie.ma at gmail.com (Fengjie Ma) Date: Tue, 5 Dec 2006 12:34:10 +0800 Subject: [Pw_forum] Compilation Problem Message-ID: Dear all, Recently I downloaded Quantum-Espresso v3.2. When I did "make pw", I found some errors as follows: I use the Intel Compiler for Linux. Error 169 at (3245:ptoolkit.F90) : This is not the name of an integer PARAMETER ^ Error 17 at (3245:ptoolkit.F90) : invalid kind parameter external subroutine PARA_DGEMV external subroutine PARA_ZGEMV external subroutine PARA_DCHOLDC external subroutine PARA_ZCHOLDC COMPLEX(DP), PARAMETER :: ONE = (1.0_DP,0.0_DP), ZERO = ( 0.0_DP, 0.0_DP ) ^ Error 169 at (3602:ptoolkit.F90) : This is not the name of an integer PARAMETER ^ Error 17 at (3602:ptoolkit.F90) : invalid kind parameter external subroutine PARA_DTRTRI external subroutine PARA_ZTRTRI COMPLEX(DP), PARAMETER :: ONE = (1.0_DP,0.0_DP), ZERO = ( 0.0_DP, 0.0_DP ) ^ Error 169 at (3760:ptoolkit.F90) : This is not the name of an integer PARAMETER ^ Error 17 at (3760:ptoolkit.F90) : invalid kind parameter external subroutine SQR_MM_CANNON REAL*8, INTENT(IN) :: alpha, beta ^ Warning 2 at (3840:ptoolkit.F90) : Type size specifiers are an extension to standard Fortran 95 REAL*8 :: a(lda,*), b(ldb,*), c(ldc,*) ^ Warning 2 at (3842:ptoolkit.F90) : Type size specifiers are an extension to standard Fortran 95 integer*8 MPI_DISPLACEMENT_CURRENT ^ Warning 2 at (248:/soft/mpi_intel/include/mpif.h) : Type size specifiers are an extension to standard Fortran 95 real*8, allocatable :: bblk(:,:), ablk(:,:) ^ Warning 2 at (3867:ptoolkit.F90) : Type size specifiers are an extension to standard Fortran 95 internal subroutine SHIFT_BLOCK REAL*8 :: blk( :, : ) ^ Warning 2 at (3976:ptoolkit.F90) : Type size specifiers are an extension to standard Fortran 95 internal subroutine SHIFT_EXCH_BLOCK REAL*8 :: blk( :, : ) ^ Warning 2 at (4039:ptoolkit.F90) : Type size specifiers are an extension to standard Fortran 95 internal subroutine EXCHANGE_BLOCK REAL*8 :: blk( :, : ) ^ Warning 2 at (4101:ptoolkit.F90) : Type size specifiers are an extension to standard Fortran 95 external subroutine SQR_TR_CANNON REAL*8 :: a(lda,*), b(ldb,*) ^ Warning 2 at (4137:ptoolkit.F90) : Type size specifiers are an extension to standard Fortran 95 integer*8 MPI_DISPLACEMENT_CURRENT ^ Warning 2 at (248:/soft/mpi_intel/include/mpif.h) : Type size specifiers are an extension to standard Fortran 95 REAL*8, ALLOCATABLE :: ablk(:,:) ^ Warning 2 at (4151:ptoolkit.F90) : Type size specifiers are an extension to standard Fortran 95 internal subroutine EXCHANGE_BLOCK REAL*8 :: blk( :, : ) ^ Warning 2 at (4211:ptoolkit.F90) : Type size specifiers are an extension to standard Fortran 95 external subroutine CYC2BLK_REDIST REAL*8 :: a(lda,*), b(ldb,*) ^ Warning 2 at (4249:ptoolkit.F90) : Type size specifiers are an extension to standard Fortran 95 integer*8 MPI_DISPLACEMENT_CURRENT ^ Warning 2 at (248:/soft/mpi_intel/include/mpif.h) : Type size specifiers are an extension to standard Fortran 95 real*8, allocatable :: rcvbuf(:,:,:) ^ Warning 2 at (4264:ptoolkit.F90) : Type size specifiers are an extension to standard Fortran 95 real*8, allocatable :: sndbuf(:,:,:) ^ Warning 2 at (4265:ptoolkit.F90) : Type size specifiers are an extension to standard Fortran 95 6 Errors compilation aborted for ptoolkit.F90 (code 1) make[1]: *** [ptoolkit.o] Error 1 make[1]: Leaving directory `/home.snfs/fjma/pw3.2/espresso-3.2/Modules' make: *** [mods] Error 2 Does anyone know how to pass through it? Thanks to your help. Yours, Ma -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061205/8ddc4a95/attachment.htm From akohlmey at cmm.chem.upenn.edu Tue Dec 5 06:06:06 2006 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 5 Dec 2006 00:06:06 -0500 (EST) Subject: [Pw_forum] Compilation Problem In-Reply-To: Message-ID: On Tue, 5 Dec 2006, Fengjie Ma wrote: FM> Dear all, FM> FM> Recently I downloaded Quantum-Espresso v3.2. When I did "make pw", I found FM> some errors as follows: FM> I use the Intel Compiler for Linux. please state version and patchlevel of the compiler. there are a large number of intel linux compilers out there with different level of brokenness... axel. FM> FM> Error 169 at (3245:ptoolkit.F90) : This is not the name of an integer FM> PARAMETER FM> ^ FM> Error 17 at (3245:ptoolkit.F90) : invalid kind parameter FM> external subroutine PARA_DGEMV FM> external subroutine PARA_ZGEMV FM> external subroutine PARA_DCHOLDC FM> external subroutine PARA_ZCHOLDC FM> COMPLEX(DP), PARAMETER :: ONE = (1.0_DP,0.0_DP), ZERO = ( 0.0_DP, 0.0_DP ) FM> ^ FM> Error 169 at (3602:ptoolkit.F90) : This is not the name of an integer FM> PARAMETER FM> ^ FM> Error 17 at (3602:ptoolkit.F90) : invalid kind parameter FM> external subroutine PARA_DTRTRI FM> external subroutine PARA_ZTRTRI FM> COMPLEX(DP), PARAMETER :: ONE = (1.0_DP,0.0_DP), ZERO = ( 0.0_DP, 0.0_DP ) FM> ^ FM> Error 169 at (3760:ptoolkit.F90) : This is not the name of an integer FM> PARAMETER FM> ^ FM> Error 17 at (3760:ptoolkit.F90) : invalid kind parameter FM> external subroutine SQR_MM_CANNON FM> FM> REAL*8, INTENT(IN) :: alpha, beta FM> ^ FM> Warning 2 at (3840:ptoolkit.F90) : Type size specifiers are an extension to FM> standard Fortran 95 FM> FM> REAL*8 :: a(lda,*), b(ldb,*), c(ldc,*) FM> ^ FM> Warning 2 at (3842:ptoolkit.F90) : Type size specifiers are an extension to FM> standard Fortran 95 FM> FM> integer*8 MPI_DISPLACEMENT_CURRENT FM> ^ FM> Warning 2 at (248:/soft/mpi_intel/include/mpif.h) : Type size specifiers are FM> an extension to standard Fortran 95 FM> FM> real*8, allocatable :: bblk(:,:), ablk(:,:) FM> ^ FM> Warning 2 at (3867:ptoolkit.F90) : Type size specifiers are an extension to FM> standard Fortran 95 FM> internal subroutine SHIFT_BLOCK FM> FM> REAL*8 :: blk( :, : ) FM> ^ FM> Warning 2 at (3976:ptoolkit.F90) : Type size specifiers are an extension to FM> standard Fortran 95 FM> internal subroutine SHIFT_EXCH_BLOCK FM> FM> REAL*8 :: blk( :, : ) FM> ^ FM> Warning 2 at (4039:ptoolkit.F90) : Type size specifiers are an extension to FM> standard Fortran 95 FM> internal subroutine EXCHANGE_BLOCK FM> FM> REAL*8 :: blk( :, : ) FM> ^ FM> Warning 2 at (4101:ptoolkit.F90) : Type size specifiers are an extension to FM> standard Fortran 95 FM> external subroutine SQR_TR_CANNON FM> FM> REAL*8 :: a(lda,*), b(ldb,*) FM> ^ FM> Warning 2 at (4137:ptoolkit.F90) : Type size specifiers are an extension to FM> standard Fortran 95 FM> FM> integer*8 MPI_DISPLACEMENT_CURRENT FM> ^ FM> Warning 2 at (248:/soft/mpi_intel/include/mpif.h) : Type size specifiers are FM> an extension to standard Fortran 95 FM> FM> REAL*8, ALLOCATABLE :: ablk(:,:) FM> ^ FM> Warning 2 at (4151:ptoolkit.F90) : Type size specifiers are an extension to FM> standard Fortran 95 FM> internal subroutine EXCHANGE_BLOCK FM> FM> REAL*8 :: blk( :, : ) FM> ^ FM> Warning 2 at (4211:ptoolkit.F90) : Type size specifiers are an extension to FM> standard Fortran 95 FM> external subroutine CYC2BLK_REDIST FM> FM> REAL*8 :: a(lda,*), b(ldb,*) FM> ^ FM> Warning 2 at (4249:ptoolkit.F90) : Type size specifiers are an extension to FM> standard Fortran 95 FM> FM> integer*8 MPI_DISPLACEMENT_CURRENT FM> ^ FM> Warning 2 at (248:/soft/mpi_intel/include/mpif.h) : Type size specifiers are FM> an extension to standard Fortran 95 FM> FM> real*8, allocatable :: rcvbuf(:,:,:) FM> ^ FM> Warning 2 at (4264:ptoolkit.F90) : Type size specifiers are an extension to FM> standard Fortran 95 FM> FM> real*8, allocatable :: sndbuf(:,:,:) FM> ^ FM> Warning 2 at (4265:ptoolkit.F90) : Type size specifiers are an extension to FM> standard Fortran 95 FM> FM> FM> FM> 6 Errors FM> compilation aborted for ptoolkit.F90 (code 1) FM> make[1]: *** [ptoolkit.o] Error 1 FM> make[1]: Leaving directory `/home.snfs/fjma/pw3.2/espresso-3.2/Modules' FM> make: *** [mods] Error 2 FM> FM> Does anyone know how to pass through it? Thanks to your help. FM> FM> Yours, FM> FM> Ma FM> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From lanhaiping at gmail.com Tue Dec 5 08:49:29 2006 From: lanhaiping at gmail.com (lan haiping) Date: Tue, 5 Dec 2006 15:49:29 +0800 Subject: [Pw_forum] about kpoints Message-ID: Dear All, I am confusing about kpoints' setting in pw calculations. I ever read Doc/INPUT_PW and related refs. There are several kpoints schemes in pw : 'automatic' ,'crystal','tippa','gamma' . For crystal case, we can specify the number of kpoints to sample BZ. Then , what i wana know is whether the kpoints list for pw.x calculate is the same as the kpoints list specified in input ? Does it ever consider system's symmtery in calculation ? I have perfomed a calculation of anatase TiO2 with 64 specified kpoints, but the output indicated that there are 164 kpoints actually for BZ sampling in the calculation . Would you please give me some comments ? Thanks . Regards, -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061205/db7db21c/attachment.htm From fengjie.ma at gmail.com Tue Dec 5 12:22:57 2006 From: fengjie.ma at gmail.com (Fengjie Ma) Date: Tue, 5 Dec 2006 19:22:57 +0800 Subject: [Pw_forum] Compilation Problem In-Reply-To: References: Message-ID: Hi axel, The complier is Intel(R) Fortran Itanium(R) Compiler for Itanium(R)-based applications Version 7.1, Build 20030814 Yours, Ma 2006/12/5, Axel Kohlmeyer : > > On Tue, 5 Dec 2006, Fengjie Ma wrote: > > FM> Dear all, > FM> > FM> Recently I downloaded Quantum-Espresso v3.2. When I did "make pw", I > found > FM> some errors as follows: > FM> I use the Intel Compiler for Linux. > > please state version and patchlevel of the compiler. there are > a large number of intel linux compilers out there with different > level of brokenness... > > axel. > > FM> > FM> Error 169 at (3245:ptoolkit.F90) : This is not the name of an integer > FM> PARAMETER > FM> > ^ > FM> Error 17 at (3245:ptoolkit.F90) : invalid kind parameter > FM> external subroutine PARA_DGEMV > FM> external subroutine PARA_ZGEMV > FM> external subroutine PARA_DCHOLDC > FM> external subroutine PARA_ZCHOLDC > FM> COMPLEX(DP), PARAMETER :: ONE = (1.0_DP,0.0_DP), ZERO = ( 0.0_DP, > 0.0_DP ) > FM> > ^ > FM> Error 169 at (3602:ptoolkit.F90) : This is not the name of an integer > FM> PARAMETER > FM> > ^ > FM> Error 17 at (3602:ptoolkit.F90) : invalid kind parameter > FM> external subroutine PARA_DTRTRI > FM> external subroutine PARA_ZTRTRI > FM> COMPLEX(DP), PARAMETER :: ONE = (1.0_DP,0.0_DP), ZERO = ( 0.0_DP, > 0.0_DP ) > FM> > ^ > FM> Error 169 at (3760:ptoolkit.F90) : This is not the name of an integer > FM> PARAMETER > FM> > ^ > FM> Error 17 at (3760:ptoolkit.F90) : invalid kind parameter > FM> external subroutine SQR_MM_CANNON > FM> > FM> REAL*8, INTENT(IN) :: alpha, beta > FM> ^ > FM> Warning 2 at (3840:ptoolkit.F90) : Type size specifiers are an > extension to > FM> standard Fortran 95 > FM> > FM> REAL*8 :: a(lda,*), b(ldb,*), c(ldc,*) > FM> ^ > FM> Warning 2 at (3842:ptoolkit.F90) : Type size specifiers are an > extension to > FM> standard Fortran 95 > FM> > FM> integer*8 MPI_DISPLACEMENT_CURRENT > FM> ^ > FM> Warning 2 at (248:/soft/mpi_intel/include/mpif.h) : Type size > specifiers are > FM> an extension to standard Fortran 95 > FM> > FM> real*8, allocatable :: bblk(:,:), ablk(:,:) > FM> ^ > FM> Warning 2 at (3867:ptoolkit.F90) : Type size specifiers are an > extension to > FM> standard Fortran 95 > FM> internal subroutine SHIFT_BLOCK > FM> > FM> REAL*8 :: blk( :, : ) > FM> ^ > FM> Warning 2 at (3976:ptoolkit.F90) : Type size specifiers are an > extension to > FM> standard Fortran 95 > FM> internal subroutine SHIFT_EXCH_BLOCK > FM> > FM> REAL*8 :: blk( :, : ) > FM> ^ > FM> Warning 2 at (4039:ptoolkit.F90) : Type size specifiers are an > extension to > FM> standard Fortran 95 > FM> internal subroutine EXCHANGE_BLOCK > FM> > FM> REAL*8 :: blk( :, : ) > FM> ^ > FM> Warning 2 at (4101:ptoolkit.F90) : Type size specifiers are an > extension to > FM> standard Fortran 95 > FM> external subroutine SQR_TR_CANNON > FM> > FM> REAL*8 :: a(lda,*), b(ldb,*) > FM> ^ > FM> Warning 2 at (4137:ptoolkit.F90) : Type size specifiers are an > extension to > FM> standard Fortran 95 > FM> > FM> integer*8 MPI_DISPLACEMENT_CURRENT > FM> ^ > FM> Warning 2 at (248:/soft/mpi_intel/include/mpif.h) : Type size > specifiers are > FM> an extension to standard Fortran 95 > FM> > FM> REAL*8, ALLOCATABLE :: ablk(:,:) > FM> ^ > FM> Warning 2 at (4151:ptoolkit.F90) : Type size specifiers are an > extension to > FM> standard Fortran 95 > FM> internal subroutine EXCHANGE_BLOCK > FM> > FM> REAL*8 :: blk( :, : ) > FM> ^ > FM> Warning 2 at (4211:ptoolkit.F90) : Type size specifiers are an > extension to > FM> standard Fortran 95 > FM> external subroutine CYC2BLK_REDIST > FM> > FM> REAL*8 :: a(lda,*), b(ldb,*) > FM> ^ > FM> Warning 2 at (4249:ptoolkit.F90) : Type size specifiers are an > extension to > FM> standard Fortran 95 > FM> > FM> integer*8 MPI_DISPLACEMENT_CURRENT > FM> ^ > FM> Warning 2 at (248:/soft/mpi_intel/include/mpif.h) : Type size > specifiers are > FM> an extension to standard Fortran 95 > FM> > FM> real*8, allocatable :: rcvbuf(:,:,:) > FM> ^ > FM> Warning 2 at (4264:ptoolkit.F90) : Type size specifiers are an > extension to > FM> standard Fortran 95 > FM> > FM> real*8, allocatable :: sndbuf(:,:,:) > FM> ^ > FM> Warning 2 at (4265:ptoolkit.F90) : Type size specifiers are an > extension to > FM> standard Fortran 95 > FM> > FM> > FM> > FM> 6 Errors > FM> compilation aborted for ptoolkit.F90 (code 1) > FM> make[1]: *** [ptoolkit.o] Error 1 > FM> make[1]: Leaving directory `/home.snfs/fjma/pw3.2/espresso-3.2 > /Modules' > FM> make: *** [mods] Error 2 > FM> > FM> Does anyone know how to pass through it? Thanks to your help. > FM> > FM> Yours, > FM> > FM> Ma > FM> > > -- > ======================================================================= > 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: /pipermail/attachments/20061205/df5373d8/attachment.htm From giannozz at nest.sns.it Tue Dec 5 13:37:43 2006 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 5 Dec 2006 13:37:43 +0100 Subject: [Pw_forum] Compilation Problem In-Reply-To: References: Message-ID: On Dec 5, 2006, at 5:34 , Fengjie Ma wrote: > Recently I downloaded Quantum-Espresso v3.2. When I did "make pw" you re-run "configure", didn't you? Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From fengjie.ma at gmail.com Wed Dec 6 06:13:00 2006 From: fengjie.ma at gmail.com (Ma Fengjie) Date: Wed, 6 Dec 2006 13:13:00 +0800 Subject: [Pw_forum] Compilation Problem References: Message-ID: <001001c718f5$35025d30$9b0aa8c0@IBMT60> Hi Axel, Thanks for you help. When I replace all "_DP" with "d0", the compilation successfully passes through this problem, but there is another one: 56 Lines Compiled cpp -P -traditional -D__LINUX64 -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA -I../include -I/soft/fftw-215/include/ -I/soft/mkl61/include/ -I/soft/mpi_intel/include/ wannier.f90 -o wannier.F90 wannier.f90:8: #include expects "fname" or make[1]: *** [wannier.o] Error 1 make[1]: Leaving directory `/home.snfs/fjma/pw3.2/espresso-3.2/Modules' make: *** [mods] Error 2 ---------------------------------------------- Institute of Theoretical Physics (ITP) Chinese Academy of Sciences (CAS) Zhong Guan Cun Dong Lu, 55 100080 Beijing, China Phone: 86-10-6264-8753 E-mail: fjma at itp.ac.cn ----- Original Message ----- From: "Axel Kohlmeyer" To: "Fengjie Ma" Sent: Tuesday, December 05, 2006 7:36 PM Subject: Re: [Pw_forum] Compilation Problem > On Tue, 5 Dec 2006, Fengjie Ma wrote: > > FM> 2006/12/5, Axel Kohlmeyer : > FM> > > FM> > On Tue, 5 Dec 2006, Fengjie Ma wrote: > FM> > FM> > FM> Hi axel, > FM> > FM> The complier is > FM> Intel(R) Fortran Itanium(R) Compiler for Itanium(R)-based > FM> applications > FM> Version 7.1, Build 20030814 > > there you go. like i suspected. this is a 'stone age' version. > there are probably some ways to work around those compilation > problems, e.g. by replacing in the line indicate the code: > COMPLEX(DP), PARAMETER :: ONE = (1.0_DP,0.0_DP), ZERO = ( 0.0_DP, 0.0_DP ) > with: > COMPLEX(DP), PARAMETER :: ONE = (1.0d0,0.0d0), ZERO = ( 0.0d0,0.0d0 ) > > but the former is valid fortran 95 syntax and should be accepted by > the compiler. it works fine with intel version 8.1 and 9.1 (which > is the current version!) and several other compilers so it may be > high time to upgrade the compiler. > > cheers, > axel. > > FM> > FM> Yours, > FM> Ma > FM> > FM> > FM> > > -- > ======================================================================= > 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 fengjie.ma at gmail.com Wed Dec 6 06:44:38 2006 From: fengjie.ma at gmail.com (Fengjie Ma) Date: Wed, 6 Dec 2006 13:44:38 +0800 Subject: [Pw_forum] Compilation Problem In-Reply-To: References: Message-ID: Hi Axel, Thanks for you help. When I replace all "_DP" with "d0", the compilation successfully passes through this problem, but there is another one: 56 Lines Compiled cpp -P -traditional -D__LINUX64 -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA -I../include -I/soft/fftw-215/include/ -I/soft/mkl61/include/ -I/soft/mpi_intel/include/ wannier.f90 -o wannier.F90 wannier.f90 :8: #include expects "fname" or make[1]: *** [wannier.o] Error 1 make[1]: Leaving directory `/home.snfs/fjma/pw3.2/espresso-3.2/Modules' make: *** [mods] Error 2 2006/12/5, Axel Kohlmeyer : > > On Tue, 5 Dec 2006, Fengjie Ma wrote: > > FM> 2006/12/5, Axel Kohlmeyer < akohlmey at cmm.chem.upenn.edu>: > FM> > > FM> > On Tue, 5 Dec 2006, Fengjie Ma wrote: > FM> > FM> > FM> Hi axel, > FM> > FM> The complier is > FM> Intel(R) Fortran Itanium(R) Compiler for > Itanium(R)-based > FM> applications > FM> Version 7.1, Build 20030814 > > there you go. like i suspected. this is a 'stone age' version. > there are probably some ways to work around those compilation > problems, e.g. by replacing in the line indicate the code: > COMPLEX(DP), PARAMETER :: ONE = (1.0_DP,0.0_DP), ZERO = ( 0.0_DP, 0.0_DP ) > with: > COMPLEX(DP), PARAMETER :: ONE = (1.0d0,0.0d0), ZERO = ( 0.0d0,0.0d0 ) > > but the former is valid fortran 95 syntax and should be accepted by > the compiler. it works fine with intel version 8.1 and 9.1 (which > is the current version!) and several other compilers so it may be > high time to upgrade the compiler. > > cheers, > axel. > > FM> > FM> Yours, > FM> Ma > FM> > FM> > FM> > > -- > ======================================================================= > 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: /pipermail/attachments/20061206/e82c899f/attachment.htm From jibiaoli at gmail.com Wed Dec 6 09:00:17 2006 From: jibiaoli at gmail.com (Clark Lee) Date: Wed, 6 Dec 2006 16:00:17 +0800 Subject: [Pw_forum] compilation error of QE 3.2 Message-ID: Hi, everyone, The following error found when compiling QE3.2 with ifort8.1 make pw ... ... ranlib clib.a make[1]: Leaving directory `/usr/local/src/espresso-3.2/clib' ( cd flib ; if test "make" = "" ; then make TLDEPS= all ; \ else make TLDEPS= all ; fi ) make[1]: Entering directory `/usr/local/src/espresso-3.2/flib' make[1]: *** No rule to make target `all'. Stop. make[1]: Leaving directory `/usr/local/src/espresso-3.2/flib' make: *** [libs] Error 2 -- Standing on the shoulders of Newton -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061206/5889c99e/attachment.htm From giannozz at nest.sns.it Wed Dec 6 11:08:23 2006 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 6 Dec 2006 11:08:23 +0100 Subject: [Pw_forum] Compilation Problem In-Reply-To: <001001c718f5$35025d30$9b0aa8c0@IBMT60> References: <001001c718f5$35025d30$9b0aa8c0@IBMT60> Message-ID: On Dec 6, 2006, at 6:13 , Ma Fengjie wrote: > cpp -P -traditional -D__LINUX64 -D__FFTW -D__USE_INTERNAL_FFTW - > D__MPI -D__PARA -I../include once again: did you re-run "./configure" ? --- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at nest.sns.it Wed Dec 6 11:14:46 2006 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 6 Dec 2006 11:14:46 +0100 Subject: [Pw_forum] compilation error of QE 3.2 In-Reply-To: References: Message-ID: On Dec 6, 2006, at 9:00 , Clark Lee wrote: > The following error found when compiling QE3.2 with ifort8.1 > [...] > make[1]: Entering directory `/usr/local/src/espresso- 3.2/flib' > make[1]: *** No rule to make target `all'. Stop. the only explanation is that you have a broken or incomplete *.tar.gz . There should be a file flib/Makefile, containing a line all: blas.a flib.a lapack_atlas.a lapack.a ptools.a Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From fengjie.ma at gmail.com Wed Dec 6 13:05:10 2006 From: fengjie.ma at gmail.com (Fengjie Ma) Date: Wed, 6 Dec 2006 20:05:10 +0800 Subject: [Pw_forum] Compilation Problem Message-ID: On Dec 6, 2006, at 6:13 , Ma Fengjie wrote: >* cpp -P -traditional -D__LINUX64 -D__FFTW -D__USE_INTERNAL_FFTW - *>* D__MPI -D__PARA -I../include * once again: did you re-run "./configure" ? Hi Paolo, yes, first I run ./configure, then I edit the make.sys and iotk/include/iotk_config.h. After all of this, I run "make pw". And following Axel's advice, I replaced all "_DP" with "d0" in ptoolkit.F90and the compilation successfully passed through this problem. Another problem that I asked this afternoon also having been solved by using "dos2unix wannier.f90". But now I meet the third problem: 128 Lines Compiled cpp -P -traditional -D__LINUX64 -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA -I../include -I/soft/fftw-215/include/ -I/soft/mkl61/include/ -I/soft/mpi_intel/include/ read_file.f90 -o read_file.F90 mpif90 -O -D__LINUX64 -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA -I../include -I/soft/fftw-215/include/ -I/soft/mkl61/include/ -I/soft/mpi_intel/include/ -I./ -I../Modules -I../iotk/src -I../PW -I../PH -I../CPV -Vaxlib -D__LINUX64 -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA -I../include -I/soft/fftw-215/include/ -I/soft/mkl61/include/ -I/soft/mpi_intel/include/ -I./ -I../Modules -I../iotk/src -I../PW -I../PH -I../CPV -c read_file.F90 -o read_file.o external subroutine READ_FILE internal subroutine SET_DIMENSIONS Error 355 : In program unit READ_FILE variable NSP has not been given a type 1 Error compilation aborted for read_file.F90 (code 1) make: *** [read_file.o] Error 1 Thanks for you help. Yours Ma -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061206/0d035c24/attachment.htm From giannozz at nest.sns.it Wed Dec 6 15:02:54 2006 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 6 Dec 2006 15:02:54 +0100 Subject: [Pw_forum] Compilation Problem In-Reply-To: References: Message-ID: <21C98C7A-DCC8-48DE-A86C-03455721D88C@nest.sns.it> On Dec 6, 2006, at 13:05 , Fengjie Ma wrote: > yes, first I run ./configure, then I edit the make.sys and iotk/ > include/iotk_config.h. you shouldn't need to modify either, if "configure" finds that "ifc" is the underlying compiler called by "mpif90". Maybe it doesn't? > Another problem that I asked this afternoon also having been solved > by using "dos2unix wannier.f90". there were unfortunately DOS ^M characters left in some files. It had been fixed but I forgot to include this fix in the distribution. > cpp -P -traditional you do not need a separate preprocessing step for ifc > -D__LINUX64 this preprocessing option doesn't exist any longer (see include/defs.h.README for a list of preprocessing options) > -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA -I../include -I/ > soft/fftw-215/include/ you do not need include files for fftw if you use the internal fft > Error 355 : In program unit READ_FILE variable NSP has not been > given a type it has, whatever the compiler says. Try to remove "ntyp => nsp," and to change the only occurrence of "ntyp" into "nsp" in PW/read_file.f90 ; maybe this confuses the compiler Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at nest.sns.it Wed Dec 6 15:08:47 2006 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 6 Dec 2006 15:08:47 +0100 Subject: [Pw_forum] Compilation Problem In-Reply-To: References: Message-ID: On Dec 5, 2006, at 12:22 , Fengjie Ma wrote: > The compiler is > Intel(R) Fortran Itanium(R) Compiler for Itanium(R)-based applications > Version 7.1, Build 20030814 I see. Then the serial compiler is probably "efc" and not "ifc" ... Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From Gianni.Profeta at aquila.infn.it Wed Dec 6 20:24:48 2006 From: Gianni.Profeta at aquila.infn.it (Gianni Profeta) Date: Wed, 6 Dec 2006 20:24:48 +0100 (CET) Subject: [Pw_forum] AIX + XML files In-Reply-To: References: Message-ID: Dear Alex, > please have a look at your make.sys file and compare the settings > that configure has picked up with the following (most important are > F90 and MPIF90, this is for parallel compilation...). there are > some subtle semantics issue, that strike only the ibm compilers > which do not seem to automatically switch to f95 mode on .f90 file > name extensions (you _have_ to use xlf95 or mpxlf95... :-( ). > I tried to change the make.sys according to your suggestions (and with different combinations of flags/options) but with no improvements and finally I installed the new 3.2 version of the code. Here is what I find (some new features): 1) with the default make.sys (the one generated by configure) and running with one k-point all is ok (as before). BUT: I find fort.17, fort.9000, fort.4 files created in the running directory (they appear to have xml tags) AND: the /tmp/Al.save/K00001/ directory's empty. 2) just increasing the number of k-points to 2, the code does not finish the first iteration (but does not crash). Thanks in advance. Gianni From jess.kondor at gmail.com Thu Dec 7 01:55:04 2006 From: jess.kondor at gmail.com (Jess Kondor) Date: Wed, 6 Dec 2006 18:55:04 -0600 Subject: [Pw_forum] Magnetic moment on each atom Message-ID: <9d7293e10612061655l2dd72da8o17755d5118d24ae1@mail.gmail.com> Hello, everyone I am studying the magnetic systems. The code (pwscf) prints absolute and total magnetization. Is there a way to get the magnetic moment of each atom in the unit cell? Thanks, JK -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061206/ee7f0165/attachment.htm From fengjie.ma at gmail.com Thu Dec 7 03:03:15 2006 From: fengjie.ma at gmail.com (Fengjie Ma) Date: Thu, 7 Dec 2006 10:03:15 +0800 Subject: [Pw_forum] Re: Compilation Problem Message-ID: Hi Paolo, Thanks again for your help. When I removed "ntyp => nsp," and replaced "ntyp" with "nsp" in PW/read_file.f90, the compilation is ok, But the fourth error appears in the last step: mpif90 -o pw.x \ pwscf.o ../Modules/atom.o ../Modules/autopilot.o ../Modules/basic_algebra_routines.o ../Modules/berry_phase.o ../Modules/bfgs_module.o ../Modules/cell_base.o ../Modules/check_stop.o ../Modules/clocks.o ../Modules/constants.o ../Modules/constraints_module.o ../Modules/control_flags.o ../Modules/electrons_base.o ../Modules/fft_base.o ../Modules/fft_scalar.o ../Modules/fft_types.o ../Modules/functionals.o ../Modules/input_parameters.o ../Modules/io_files.o ../Modules/io_global.o ../Modules/ions_base.o ../Modules/ions_nose.o ../Modules/kind.o ../Modules/mp_global.o ../Modules/mp_wave.o ../Modules/mp.o ../Modules/metadyn_base.o ../Modules/metadyn_io.o ../Modules/metadyn_vars.o ../Modules/path_base.o ../Modules/path_formats.o ../Modules/path_variables.o ../Modules/path_opt_routines.o ../Modules/path_io_routines.o ../Modules/path_reparametrisation.o ../Modules/parallel_include.o ../Modules/parameters.o ../Modules/parser.o ../Modules/printout_base.o ../Modules/pseudo_types.o ../Modules/ptoolkit.o ../Modules/random_numbers.o ../Modules/read_cards.o ../Modules/read_namelists.o ../Modules/read_upf.o ../Modules/read_uspp.o ../Modules/recvec.o ../Modules/shmem_include.o ../Modules/splinelib.o ../Modules/stick_base.o ../Modules/task_groups.o ../Modules/timestep.o ../Modules/uspp.o ../Modules/version.o ../Modules/wavefunctions.o ../Modules/wave_base.o ../Modules/xml_io_base.o libpw.a ../flib/ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a -lmkl_lapack -L/soft/mkl61/lib/64/ -lmkl_ipf -lguide -lpthread -L/soft/mpi_intel/lib/ -lmpif90 -lmpi -lfmpi ld: Warning: size of symbol `MODULE$control_flags_1' changed from 196 to 492 in ../Modules/control_flags.o ld: Warning: size of symbol `MODULE$reciprocal_vectors_1' changed from 352 to 1016 in ../Modules/recvec.o ../Modules/berry_phase.o: In function `berry_phase$$ln_setup_': ../Modules/berry_phase.o(.text+0xd2): undefined reference to `ln_alloc_' ../Modules/berry_phase.o(.text+0x212): undefined reference to `ln_set_' ../Modules/berry_phase.o(.text+0x232): undefined reference to `ln_activate_' ../Modules/berry_phase.o: In function `berry_phase$$ln_closeup_': ../Modules/berry_phase.o(.text+0x322): undefined reference to `ln_dealloc_' ../Modules/berry_phase.o: In function `berry_phase$$indi_of_ig_': ../Modules/berry_phase.o(.text+0x61c2): undefined reference to `ln_ind_' ../Modules/berry_phase.o(.text+0x6362): undefined reference to `ln_ind_' ../Modules/berry_phase.o(.text+0x63e2): undefined reference to `ln_ind_' ../Modules/berry_phase.o(.text+0x6452): undefined reference to `ln_ind_' ../Modules/berry_phase.o(.text+0x6572): undefined reference to `ln_ind_' ../Modules/berry_phase.o(.text+0x6602): more undefined references to `ln_ind_' follow make[1]: *** [pw.x] Error 1 make[1]: Leaving directory `/home.snfs/fjma/pw3.2/espresso-3.2/PW' make: *** [pw] Error 2 Yours, Ma -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061207/8db4c34c/attachment.htm From s305igun at mail.chem.itb.ac.id Thu Dec 7 07:35:29 2006 From: s305igun at mail.chem.itb.ac.id (Rahmat Gunawan) Date: Thu, 7 Dec 2006 13:35:29 +0700 (WIT) Subject: [Pw_forum] ibrav=4, what kind of it's k_point? In-Reply-To: References: Message-ID: <1357.167.205.72.36.1165473329.squirrel@webmail.chem.itb.ac.id> Dear Pw_Forum I would like to understand about k_point, I have my crystal inpit: ibrav=4, and I run 'relax' my pw.x and give not good result.. and this is my input K_POINTS tpiba 9 0.000000000 0.000000000 0.000000000 1.00 0.062500000 0.036084392 0.000000000 6.00 0.125000000 0.072168784 0.000000000 6.00 0.187500000 0.108253175 0.000000000 6.00 0.250000000 0.433012702 0.000000000 6.00 0.250000000 0.433012702 0.000000000 6.00 0.312500000 0.469097094 0.000000000 12.00 0.375000000 0.505181486 0.000000000 6.00 0.312500000 0.541265877 0.000000000 6.00 It is problem for me, so would You like to give suggest for my hydorgen-graphite system input? I would like to thanks very much to You in this PW_Forum Success for your research Sincerely Yours Rahmat Gunawan PostGraduate Student Dept. of Chemistry Bandung Institute of Technology Indonesia From ALAIN.ALLOUCHE at UP.UNIV-MRS.FR Thu Dec 7 07:49:33 2006 From: ALAIN.ALLOUCHE at UP.UNIV-MRS.FR (Alain Allouche) Date: Thu, 7 Dec 2006 07:49:33 +0100 Subject: [Pw_forum] iotk_write_begin In-Reply-To: <20061207063602.12578.41546.Mailman@democritos.sissa.it> References: <20061207063602.12578.41546.Mailman@democritos.sissa.it> Message-ID: Hi, everyone, Can somebody explain this error in espresso.3.2 pw.x (IBM AIX) at the end of job, it seems to be related to the "save" process Thanks ############################################################# # UNRECOVERABLE ERROR (ierr=1) # ERROR IN: iotk_write_begin (iotk_write.spp:65) # CVS Revision: 1.2 # Wrong tag name name=Be+_MASS # ERROR IN: iotk_write_dat (iotk_dat.spp:234) # CVS Revision: 1.3 ######################################################################## ################################################ From giannozz at nest.sns.it Thu Dec 7 10:48:45 2006 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 7 Dec 2006 10:48:45 +0100 Subject: [Pw_forum] Re: Compilation Problem In-Reply-To: References: Message-ID: <5776C105-7351-4C86-A933-A311A741508D@nest.sns.it> On Dec 7, 2006, at 3:03 , Fengjie Ma wrote: > > ld: Warning: size of symbol `MODULE$control_flags_1' changed from > 196 to 492 in ../Modules/control_flags.o > ld: Warning: size of symbol `MODULE$reciprocal_vectors_1' changed > from 352 to 1016 in ../Modules/recvec.o these warning have always been present in v.7 of the intel compiler and shoukld be harmless > ../Modules/berry_phase.o(.text+0xd2): undefined reference to > `ln_alloc_' > ../Modules/berry_phase.o(.text+0x212): undefined reference to > `ln_set_' > ../Modules/berry_phase.o(.text+0x232): undefined reference to > `ln_activate_' > ../Modules/berry_phase.o: In function `berry_phase$$ln_closeup_': > ../Modules/berry_phase.o(.text+0x322): undefined reference to > `ln_dealloc_' > ../Modules/berry_phase.o(.text+0x61c2): undefined reference to > `ln_ind_' in include/c_defs.h, there are two lines that look like: #define F77_FUNC(name,NAME) name ## _ #define F77_FUNC_(name,NAME) name ## __ or something like this. Set the correct number of underscores at the end and recompile. The module "berry_phase" is not actually used. Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From jhashemifar at gmail.com Thu Dec 7 11:24:26 2006 From: jhashemifar at gmail.com (Javad hashemifar) Date: Thu, 7 Dec 2006 11:24:26 +0100 Subject: [Pw_forum] Magnetic moment on each atom In-Reply-To: <9d7293e10612061655l2dd72da8o17755d5118d24ae1@mail.gmail.com> References: <9d7293e10612061655l2dd72da8o17755d5118d24ae1@mail.gmail.com> Message-ID: <2fb18d9f0612070224y6187d0ceqbb620af4d5c4380b@mail.gmail.com> I have not much experience with pwscf and I am at the first steps of using it, but I think you can use projwfc.x to calculate the atomic magnetic moments as well as partial density of states. After a normal scf, you have to do a non-scf calculation and then dos.x should be executed. Finally by executing projwfc.x, and looking at its output you can find the number of up and down electrons of each atom (so called "Lowdin" charges). By subtracting these values you will get the atomic magnetic moments. I hope this procedure is correct. If not, more expert users may correct it. Best regards Javad Hashemifar permanent: Isfahan University of Technology, Iran current: university of Duisburg-Essen, Germany On 12/7/06, Jess Kondor wrote: > Hello, everyone > > I am studying the magnetic systems. The code (pwscf) prints absolute and > total magnetization. Is there a way to get the magnetic moment of each atom > in the unit cell? > > Thanks, > JK > > > -- ====================================== Seyed Javad Hashemifar, Ph.D. [current:] Tel:+49-203-3794743 Fax:+49-203-3794742 Fachbereich Physik, Universitat Duisburg-Essen 47048 Dusiburg, Germany [permanent:] Tel: +98-311-3912375 Fax: +98-311-3912376 Physics Department, Isfahan University of Technology 84156 Isfahan, Iran --------------------------------------------------------------------------- From ferretti.andrea at unimore.it Thu Dec 7 11:38:46 2006 From: ferretti.andrea at unimore.it (Andrea Ferretti) Date: Thu, 7 Dec 2006 11:38:46 +0100 (CET) Subject: [Pw_forum] iotk_write_begin In-Reply-To: References: <20061207063602.12578.41546.Mailman@democritos.sissa.it> Message-ID: > Hi, everyone, > Can somebody explain this error in espresso.3.2 pw.x (IBM AIX) at the end of > job, it seems to be related to the "save" process > > ############################################################# > # UNRECOVERABLE ERROR (ierr=1) > # ERROR IN: iotk_write_begin (iotk_write.spp:65) > # CVS Revision: 1.2 > # Wrong tag name > name=Be+_MASS > # ERROR IN: iotk_write_dat (iotk_dat.spp:234) > # CVS Revision: 1.3 The "+" character is not allowed in tag names of iotk (but probably this is taken from xml standard)... basically, you should define the name atomic type "Be+" in a different way... the list of allowed chars (more or less all of them except "+" and few others), is defined in iotk/srciotk_base.f90 variable: iotk_namchar around lines 110-130 cheers Andrea -- Andrea Ferretti National Research Center S3, CNR-INFM ( http://s3.infm.it ) Dipartimento di Fisica, Universita' di Modena e Reggio Emilia Via Campi 213/A I-41100 Modena, Italy Tel: +39 059 2055301 Fax: +39 059 374794 Skype: andrea_ferretti E-mail: ferretti.andrea at unimore.it URL: http://www.nanoscience.unimo.it Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html From giannozz at nest.sns.it Thu Dec 7 12:40:06 2006 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 7 Dec 2006 12:40:06 +0100 Subject: [Pw_forum] about kpoints In-Reply-To: References: Message-ID: <039CBA9C-CDB7-4793-BD86-A88A9F1062C4@nest.sns.it> On Dec 5, > I have perfomed a calculation of anatase TiO2 with 64 specified > kpoints, but the output indicated that there are 164 kpoints actually > for BZ sampling in the calculation . the list of k-points you give should include only k-points in the Irreducible Brillouin Zone, assuming the ful symmetry of the lattice. If the symmetry of the crystal is lower than this, the code will generate additional k-points Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From a0kara01 at phys.ksu.edu Sat Dec 9 01:42:03 2006 From: a0kara01 at phys.ksu.edu (Kara, Abdelkader) Date: Fri, 8 Dec 2006 18:42:03 -0600 Subject: [Pw_forum] scaling on clusters with different communication types Message-ID: Dear all, Greatings. I will appreciate it very much if you can share with me your experience of running pwscf on clusters with different communication hardware. I am interested in the scaling with the number of CPU's for the following 3 different communication types: 1)gigabit ethernet 2) myrinet 3) InfiniBand Thank you very much for your input on this matter Kader Kara Physics Department University of Central Florida From akohlmey at cmm.chem.upenn.edu Sat Dec 9 03:47:09 2006 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Fri, 8 Dec 2006 21:47:09 -0500 (EST) Subject: [Pw_forum] scaling on clusters with different communication types In-Reply-To: Message-ID: On Fri, 8 Dec 2006, Kara, Abdelkader wrote: AK> Dear all, AK> AK> Greatings. AK> AK> I will appreciate it very much if you can share with me your experience AK> of running pwscf on clusters with different communication hardware. AK> I am interested in the scaling with the number of CPU's for the following 3 AK> different communication types: AK> 1)gigabit ethernet AK> 2) myrinet AK> 3) InfiniBand scaling depends a lot on the kind of jobs you intend to run. pw.x scales almost independendly and very well across NEB images and k-points even with gigabit ethernet. on top of that you can parallelize across g-space, which is much more demanding in terms of communication bandwidth and latency. in this case scaling across gigabit is limited to a few nodes. in-node performance is governed by available memory bandwidth wich results in hyper-threading being conter-productive, multi-core cpus having reduced efficiency (depending on job size, i.e. cache efficiency) and opteron cpus due to dedicated per-cpu memory busses scaling better than intel (xeon). only very recent intel (woodcrest) xeon cpus have been demonstrated to have a somewhat better performance and price/performance ratio. please note, that these are some general trends observed from some usage patterns that may not translate to your needs. also presence of a per-node local scratch area or absence impacts the performance. using a NFS filesystem for temporary storage usually results in degraded performance. basically, the larger your systems and the fewer k-points you need use, the more important a fast interconnect becomes. performance between infiniband and myrinet solutions is more or less equivalent when compared with gigabit. thus using older/obsolete hardware can be a bargain. cheers, axel. AK> AK> Thank you very much for your input on this matter AK> AK> Kader Kara AK> AK> Physics Department AK> University of Central Florida AK> _______________________________________________ AK> Pw_forum mailing list AK> Pw_forum at pwscf.org AK> http://www.democritos.it/mailman/listinfo/pw_forum AK> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From akohlmey at cmm.chem.upenn.edu Sat Dec 9 04:01:56 2006 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Fri, 8 Dec 2006 22:01:56 -0500 (EST) Subject: [Pw_forum] AIX + XML files In-Reply-To: Message-ID: On Wed, 6 Dec 2006, Gianni Profeta wrote: dear gianni, GP> I tried to change the make.sys according to your suggestions (and with GP> different combinations of flags/options) but with no improvements and GP> finally I installed the new 3.2 version of the code. GP> Here is what I find (some new features): GP> GP> 1) with the default make.sys (the one generated by configure) and running GP> with one k-point all is ok (as before). GP> BUT: I find fort.17, fort.9000, fort.4 files created in the running GP> directory (they appear to have xml tags) GP> AND: the /tmp/Al.save/K00001/ directory's empty. this is _very_ strange. it almost looks as if your compiler miscompiles some files. can you check whether the compilers on that machine are up-to-date (within reason). you may try copying install/Make.power5-aix-parallel over your make.sys and adapting this one. please make sure that after every change to make.sys you run 'make clean' so that all objects are compiled with the same settings (which may take some patience ... :-( ) ciao, axel. GP> 2) just increasing the number of k-points to 2, the code does not finish GP> the first iteration (but does not crash). GP> Thanks in advance. GP> Gianni GP> _______________________________________________ GP> Pw_forum mailing list GP> Pw_forum at pwscf.org GP> http://www.democritos.it/mailman/listinfo/pw_forum GP> -- ======================================================================= 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 sanjeev0302 at rediffmail.com Sat Dec 9 05:44:31 2006 From: sanjeev0302 at rediffmail.com (Sanjeev Kumar Gupta) Date: 9 Dec 2006 04:44:31 -0000 Subject: [Pw_forum] problem with k-points Message-ID: <20061209044431.6599.qmail@webmail54.rediffmail.com> Respected sir, i am sanjeev gupta, from india, working DFT calculation via Quantum-Espresso-3.1.1. I have doubts with k-ponits, 1)How we choose k-points for diiferent system? 2)Is possible fermi energy negative for noble nitrides? 3)Is neccessary same k-points for scf and nscf cycle or phX,phL and phG.? with regards sanjeev gupta ==================================================== Sanjeev Kumar Gupta Junior Research Fellow (DAE-BRNS) Computational Condensed Matter Physics Lab.(CCMP) Department of Physics, Faculty of Science, The M.S.University of Baroda, Vadodara - 390 002. Ph.No: +91-265-279 5339 (O) extn: 30-25 mobile:09374616019 Email: sanjeev0302 at rediffmail.com sanjeev0302 at yahoo.co.in skgupta-phy at msubaroda.ac.in ==================================================== Residential Address- Dr. Vikram Sarabhai Hall, Room No.-95, Boys' Hostel,M.S.University Campus, Pratapgunj,Vadodara-390 002,Gujarat,INDIA -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061209/1bf9cd64/attachment.htm From gaoguoying at gmail.com Sat Dec 9 07:55:42 2006 From: gaoguoying at gmail.com (Guoying Gao) Date: Sat, 9 Dec 2006 14:55:42 +0800 Subject: [Pw_forum] questions after compile Message-ID: <6234c0c60612082255l676097ecib60997aacc0e14ef@mail.gmail.com> Dear everyone, While I am compiling the espresso-2.15 code,there is no mistake. But when I run scf calculation,in the output file, it writes as follows: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from cfts_3 : error # 1 routine called by wrong architecture %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Does anyone know the reason for this? Any answers will be welcomed. Thanks in advance! Gao From akohlmey at cmm.chem.upenn.edu Sat Dec 9 14:37:18 2006 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sat, 9 Dec 2006 08:37:18 -0500 (EST) Subject: [Pw_forum] questions after compile In-Reply-To: <6234c0c60612082255l676097ecib60997aacc0e14ef@mail.gmail.com> Message-ID: On Sat, 9 Dec 2006, Guoying Gao wrote: dear gao, GG> Dear everyone, GG> While I am compiling the espresso-2.15 code,there is no mistake. But version 2.1.5 is old and no longer supported so nobody will fix and bugs in it and you are recommended to not start any new projects with it. version 3.2 was released recently. GG> when I run scf calculation,in the output file, it writes as follows: GG> GG> GG> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% GG> from cfts_3 : error # 1 GG> routine called by wrong architecture GG> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% GG> GG> GG> Does anyone know the reason for this? Any answers will be welcomed. please always check the mailing list archives for that (or stick your error message into google with a site:democritos.it added). most likely you have a broken preprocessor in your (old/unpatched) compiler. see e.g.: http://www.democritos.it/pipermail/pw_forum/2006-February/003662.html ciao, axel. GG> Thanks in advance! GG> Gao GG> _______________________________________________ GG> Pw_forum mailing list GG> Pw_forum at pwscf.org GG> http://www.democritos.it/mailman/listinfo/pw_forum GG> -- ======================================================================= 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 a0kara01 at phys.ksu.edu Sat Dec 9 17:04:40 2006 From: a0kara01 at phys.ksu.edu (Kara, Abdelkader) Date: Sat, 9 Dec 2006 10:04:40 -0600 Subject: [Pw_forum] scaling on clusters with different communication types References: Message-ID: Thanks Axel for your valuable reply. I am actually looking for a quantitative comparison. I want to know if by using the infiniband or myrinet one can push the good (quasilinear) scaling to a higher number of CPU's. If someone did any benchmarking, I will appreciate your input. Thanks again Kader Kara UCF ________________________________ From: Axel Kohlmeyer [mailto:akohlmey at cmm.chem.upenn.edu] Sent: Fri 12/8/2006 8:47 PM To: Kara, Abdelkader Cc: pw_forum at pwscf.org Subject: Re: [Pw_forum] scaling on clusters with different communication types On Fri, 8 Dec 2006, Kara, Abdelkader wrote: AK> Dear all, AK> AK> Greatings. AK> AK> I will appreciate it very much if you can share with me your experience AK> of running pwscf on clusters with different communication hardware. AK> I am interested in the scaling with the number of CPU's for the following 3 AK> different communication types: AK> 1)gigabit ethernet AK> 2) myrinet AK> 3) InfiniBand scaling depends a lot on the kind of jobs you intend to run. pw.x scales almost independendly and very well across NEB images and k-points even with gigabit ethernet. on top of that you can parallelize across g-space, which is much more demanding in terms of communication bandwidth and latency. in this case scaling across gigabit is limited to a few nodes. in-node performance is governed by available memory bandwidth wich results in hyper-threading being conter-productive, multi-core cpus having reduced efficiency (depending on job size, i.e. cache efficiency) and opteron cpus due to dedicated per-cpu memory busses scaling better than intel (xeon). only very recent intel (woodcrest) xeon cpus have been demonstrated to have a somewhat better performance and price/performance ratio. please note, that these are some general trends observed from some usage patterns that may not translate to your needs. also presence of a per-node local scratch area or absence impacts the performance. using a NFS filesystem for temporary storage usually results in degraded performance. basically, the larger your systems and the fewer k-points you need use, the more important a fast interconnect becomes. performance between infiniband and myrinet solutions is more or less equivalent when compared with gigabit. thus using older/obsolete hardware can be a bargain. cheers, axel. AK> AK> Thank you very much for your input on this matter AK> AK> Kader Kara AK> AK> Physics Department AK> University of Central Florida AK> _______________________________________________ AK> Pw_forum mailing list AK> Pw_forum at pwscf.org AK> http://www.democritos.it/mailman/listinfo/pw_forum AK> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From s305igun at mail.chem.itb.ac.id Sat Dec 9 16:53:08 2006 From: s305igun at mail.chem.itb.ac.id (Rahmat Gunawan) Date: Sat, 9 Dec 2006 22:53:08 +0700 (WIT) Subject: [Pw_forum] problem in k-points of hydrogen-graphite system In-Reply-To: References: <6234c0c60612082255l676097ecib60997aacc0e14ef@mail.gmail.com> Message-ID: <35689.167.205.72.2.1165679588.squirrel@webmail.chem.itb.ac.id> Dear PW_Forum I would like to thank to Pw_forum, but I still have problem in our input, so our output via ghostview (graphitebands.ps) is not good. Would You like to teach us, how to write good input k-point of graphite and hydrogen-graphite system (crystal, ibrav=4, number k-points {crystal})? Please help us.. Thanks very much, success for your excellent research project Sincerely yours Rahmat Gunawan PostGraduate students Lab of Theoretical Chemistry Dept. of Chemistry Bandung Institute of Technology Indonesia From eminekb at yahoo.com Sat Dec 9 23:10:36 2006 From: eminekb at yahoo.com (e kb) Date: Sat, 9 Dec 2006 14:10:36 -0800 (PST) Subject: [Pw_forum] phonon calc. for fcc at X In-Reply-To: Message-ID: <196831.65395.qm@web34811.mail.mud.yahoo.com> Dear QE users, I am performing phonon calculations for a zinc blende structure, I calculated the frequencies at high symmetry points, evaluating a single point at each time. So I followed the procedure of scf, nscf and ph.x calculation one by one for L(0.5 0.5 0.5) - Gamma - X(0,0,1) - X(0,1,1) points. In these calculations every parameter (else than q-vector in &phonon list in nscf calculation and phonon card for ph.x input of course) is kept fixed. Although I expect the frequencies at two X points - (0,0,1) and (0,1,1) - to be the same, the difference in TA modes' frequencies are around 30 cm-1, in the other ones, around 5 cm-1. I would like to attribute this to unconverged lattice parameters, cut off energies or thresholds etc. but what I do not understand is why the program treats these two points differently, although they should be equivalent. So I expect to see the same value for frequency at these points, even if it is wrong, highly negative, or sth else that it should not be. I will appreciate any answers. Thank you. Emine Kucukbenli --------------------------------- Everyone is raving about the all-new Yahoo! Mail beta. -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061209/e9b4ec74/attachment.htm From akohlmey at cmm.chem.upenn.edu Sun Dec 10 01:55:05 2006 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sat, 9 Dec 2006 19:55:05 -0500 (EST) Subject: [Pw_forum] scaling on clusters with different communication types In-Reply-To: Message-ID: On Sat, 9 Dec 2006, Kara, Abdelkader wrote: KK> Thanks Axel for your valuable reply. KK> I am actually looking for a quantitative comparison. as i wrote before, this depends a _lot_ on the kind of jobs you intend to run. please provide a representative input file, and ask people to run it on hardware you are interested in. quantitative data, that is irrelevant to your interests is worthless. KK> I want to know if by using the infiniband or myrinet one can push KK> the good (quasilinear) scaling to a higher number of CPU's. If KK> someone did any benchmarking, I will appreciate your input. this is _exactly_ what i wrote: once you run out of k-points and/or NEB images to parallelize over, you _can_ parallelize the G/R-space part. over gigabit ethernet this works for a few more cpu cores (4-10 depending on system size). if you want to push further you _have_ to have a low latency network (i.e. myrinet or infiniband or dolphin/SCI or Quadrics or NUMA-link or SeaStar or ...) since the G-space parallelization has a lot of latency sensitive all-to-all communication. how _far_ you can push it then depends on the system size and the relative cpu/memory speed your input and many, many other details. note, that different programs and/or algorithms in the quantum espresso package are parrelelize to a different degree and amdahl's law dictates that you can only scale as much as the amount of parallelism of the code allows, regardless of the speed of the interconnect. e.g. a while ago, i've been able to run a 272 atom, 560 electron pw.x job with a 4x4x4 MP-kpoint mesh across 768 processors on a cray xt3 (using some special tricks to reduce file i/o since that machine hase no local disk at all). but i don't expect most typical pw.x jobs to scale that far and it only works because the cray xt3 has a special 3d-torus network and a lightweight kernel, that provide a high aggregate bandwith and avoid all kinds of 'OS noise' that ususally limit scaling on PC clusters. there have been reports for running with decent speedup across even more cpus (by andrea ferretti, IIRC). quite a while ago, carlo sbraccia was posting some benchmark inputs for pw.x and asked people run them and post the results. i don't know how applicable those numbers will be to you (see above and because of optimizations of the code and new hardware). please check the mailing list archives. cheers, axel. KK> KK> Thanks again KK> KK> Kader Kara KK> UCF KK> KK> ________________________________ KK> KK> From: Axel Kohlmeyer [mailto:akohlmey at cmm.chem.upenn.edu] KK> Sent: Fri 12/8/2006 8:47 PM KK> To: Kara, Abdelkader KK> Cc: pw_forum at pwscf.org KK> Subject: Re: [Pw_forum] scaling on clusters with different communication types KK> KK> KK> KK> On Fri, 8 Dec 2006, Kara, Abdelkader wrote: KK> KK> AK> Dear all, KK> AK> KK> AK> Greatings. KK> AK> KK> AK> I will appreciate it very much if you can share with me your experience KK> AK> of running pwscf on clusters with different communication hardware. KK> AK> I am interested in the scaling with the number of CPU's for the following 3 KK> AK> different communication types: KK> AK> 1)gigabit ethernet KK> AK> 2) myrinet KK> AK> 3) InfiniBand KK> KK> scaling depends a lot on the kind of jobs you intend to run. KK> KK> pw.x scales almost independendly and very well across NEB KK> images and k-points even with gigabit ethernet. on top of KK> that you can parallelize across g-space, which is much more KK> demanding in terms of communication bandwidth and latency. KK> in this case scaling across gigabit is limited to a few KK> nodes. in-node performance is governed by available memory KK> bandwidth wich results in hyper-threading being conter-productive, KK> multi-core cpus having reduced efficiency (depending on job KK> size, i.e. cache efficiency) and opteron cpus due to dedicated KK> per-cpu memory busses scaling better than intel (xeon). only KK> very recent intel (woodcrest) xeon cpus have been demonstrated KK> to have a somewhat better performance and price/performance ratio. KK> KK> please note, that these are some general trends observed from KK> some usage patterns that may not translate to your needs. KK> also presence of a per-node local scratch area or absence KK> impacts the performance. using a NFS filesystem for temporary KK> storage usually results in degraded performance. KK> KK> basically, the larger your systems and the fewer k-points KK> you need use, the more important a fast interconnect becomes. KK> performance between infiniband and myrinet solutions is KK> more or less equivalent when compared with gigabit. thus KK> using older/obsolete hardware can be a bargain. KK> KK> cheers, KK> axel. KK> KK> AK> KK> AK> Thank you very much for your input on this matter KK> AK> KK> AK> Kader Kara KK> AK> KK> AK> Physics Department KK> AK> University of Central Florida KK> AK> _______________________________________________ KK> AK> Pw_forum mailing list KK> AK> Pw_forum at pwscf.org KK> AK> http://www.democritos.it/mailman/listinfo/pw_forum KK> AK> KK> KK> -- KK> ======================================================================= KK> Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu KK> Center for Molecular Modeling -- University of Pennsylvania KK> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 KK> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 KK> ======================================================================= KK> If you make something idiot-proof, the universe creates a better idiot. KK> KK> KK> KK> _______________________________________________ KK> Pw_forum mailing list KK> Pw_forum at pwscf.org KK> http://www.democritos.it/mailman/listinfo/pw_forum KK> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From akohlmey at cmm.chem.upenn.edu Sun Dec 10 02:00:23 2006 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sat, 9 Dec 2006 20:00:23 -0500 (EST) Subject: [Pw_forum] problem in k-points of hydrogen-graphite system In-Reply-To: <35689.167.205.72.2.1165679588.squirrel@webmail.chem.itb.ac.id> Message-ID: On Sat, 9 Dec 2006, Rahmat Gunawan wrote: RG> Dear PW_Forum RG> I would like to thank to Pw_forum, but I still have problem in our input, RG> so our output via ghostview (graphitebands.ps) is not good. please explain in which way you deem the results to be not good. RG> Would You like to teach us, how to write good input k-point of graphite RG> and hydrogen-graphite system (crystal, ibrav=4, number k-points RG> {crystal})? please post an input example and explain what you want to achieve. none of us here can see what you have tried and why you think it may have failed. RG> Please help us.. please help _us_ to help you. cheers, axel. RG> RG> Thanks very much, success for your excellent research project RG> RG> Sincerely yours RG> RG> Rahmat Gunawan RG> PostGraduate students RG> Lab of Theoretical Chemistry RG> Dept. of Chemistry RG> Bandung Institute of Technology RG> Indonesia RG> _______________________________________________ RG> Pw_forum mailing list RG> Pw_forum at pwscf.org RG> http://www.democritos.it/mailman/listinfo/pw_forum RG> -- ======================================================================= 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 Dec 10 10:34:59 2006 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 10 Dec 2006 10:34:59 +0100 Subject: [Pw_forum] phonon calc. for fcc at X In-Reply-To: <196831.65395.qm@web34811.mail.mud.yahoo.com> References: <196831.65395.qm@web34811.mail.mud.yahoo.com> Message-ID: Emine: (001) and (011) are *NOT* two "X" points in the FCC Brillouin zone. The difference between the second and the first (010) is *NOT* a reciprocal-space vector. If it was, X would also be, which you will agree it is not. As a matter of fact, (011) has its own nickname (it is called "K"). No surprise, therefore, that frequencies @K are different from frequencies @X. Are these arguments clear and convincing enough? Stefano On Dec 9, 2006, at 11:10 PM, e kb wrote: > Dear QE users, > I am performing phonon calculations for a zinc blende structure, > I calculated the frequencies at high symmetry points, evaluating a > single point at each time. > So I followed the procedure of scf, nscf and ph.x calculation one > by one for L(0.5 0.5 0.5) - Gamma - X(0,0,1) - X(0,1,1) points. > In these calculations every parameter (else than q-vector in > &phonon list in nscf calculation and phonon card for ph.x input of > course) is kept fixed. > > Although I expect the frequencies at two X points - (0,0,1) and > (0,1,1) - to be the same, > the difference in TA modes' frequencies are around 30 cm-1, > in the other ones, around 5 cm-1. > > I would like to attribute this to unconverged lattice parameters, > cut off energies or thresholds etc. but what I do not understand is > why the program treats these two points differently, although they > should be equivalent. So I expect to see the same value for > frequency at these points, even if it is wrong, highly negative, or > sth else that it should not be. > > I will appreciate any answers. > Thank you. > > Emine Kucukbenli > > > > Everyone is raving about the all-new Yahoo! Mail beta. --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061210/f3341524/attachment.htm From eminekb at yahoo.com Sun Dec 10 14:46:36 2006 From: eminekb at yahoo.com (e kb) Date: Sun, 10 Dec 2006 05:46:36 -0800 (PST) Subject: [Pw_forum] phonon calc. for fcc at X In-Reply-To: Message-ID: <175910.68037.qm@web34802.mail.mud.yahoo.com> Thank you for your answer Stefano, Of course this explains the different frequencies, and that also means that I misunderstand the kpoints given in example 5, about band structure for an fcc, and Dr. Marzari's explanation to another QE user, who was confused like me. http://www.democritos.it/pipermail/pw_forum/2006-June/004365.html Thank you again, Emine Kucukbenli Stefano Baroni wrote: Emine: (001) and (011) are *NOT* two "X" points in the FCC Brillouin zone. The difference between the second and the first (010) is *NOT* a reciprocal-space vector. If it was, X would also be, which you will agree it is not. As a matter of fact, (011) has its own nickname (it is called "K"). No surprise, therefore, that frequencies @K are different from frequencies @X. Are these arguments clear and convincing enough? Stefano On Dec 9, 2006, at 11:10 PM, e kb wrote: Dear QE users, I am performing phonon calculations for a zinc blende structure, I calculated the frequencies at high symmetry points, evaluating a single point at each time. So I followed the procedure of scf, nscf and ph.x calculation one by one for L(0.5 0.5 0.5) - Gamma - X(0,0,1) - X(0,1,1) points. In these calculations every parameter (else than q-vector in &phonon list in nscf calculation and phonon card for ph.x input of course) is kept fixed. Although I expect the frequencies at two X points - (0,0,1) and (0,1,1) - to be the same, the difference in TA modes' frequencies are around 30 cm-1, in the other ones, around 5 cm-1. I would like to attribute this to unconverged lattice parameters, cut off energies or thresholds etc. but what I do not understand is why the program treats these two points differently, although they should be equivalent. So I expect to see the same value for frequency at these points, even if it is wrong, highly negative, or sth else that it should not be. I will appreciate any answers. Thank you. Emine Kucukbenli --------------------------------- Everyone is raving about the all-new Yahoo! Mail beta. --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html --------------------------------- Check out the all-new Yahoo! Mail beta - Fire up a more powerful email and get things done faster. -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061210/6f5e3d22/attachment.htm From babazade at gmail.com Sun Dec 10 15:04:25 2006 From: babazade at gmail.com (Amin Babazadeh) Date: Sun, 10 Dec 2006 17:34:25 +0330 Subject: [Pw_forum] use doual core In-Reply-To: References: <7b6913e90611220734s15038d2ei36e1e7a28166f146@mail.gmail.com> <002e01c71207$5e733cb0$1d00a8c0@solarflare> <005f01c715ed$4104e220$1d00a8c0@solarflare> Message-ID: Dear friends I am so sorry for this but i couldn't solve my problem. i installed lam 7.1.2 in my computer and i didn't change the installation PATH. after that i configure the espresso.this file has been made. # make.sys. Generated from make.sys.in by configure. # compilation rules .SUFFIXES : .SUFFIXES : .o .c .f .f90 # most fortran compilers can directly preprocess c-like directives: use # $(MPIF90) $(F90FLAGS) -c $< # if explicit preprocessing by the C preprocessor is needed, use: # $(CPP) $(CPPFLAGS) $< -o $*.F90 # $(MPIF90) $(F90FLAGS) -c $*.F90 -o $*.o # remember the tabulator in the first column !!! .f90.o: $(MPIF90) $(F90FLAGS) -c $< # .f.o and .c.o: do not modify .f.o: $(F77) $(FFLAGS) -c $< .c.o: $(CC) $(CFLAGS) -c $< # DFLAGS = precompilation options (possible arguments to -D and -U) # used by the C compiler and preprocessor # FDFLAGS = as DFLAGS, for the f90 compiler # See include/defs.h.README for a list of options and their meaning # With the exception of IBM xlf, FDFLAGS = $(DFLAGS) # For IBM xlf, FDFLAGS is the same as DFLAGS with separating commas DFLAGS = -D__INTEL -D__FFTW -D__USE_INTERNAL_FFTW FDFLAGS = $(DFLAGS) # IFLAGS = how to locate directories where files to be included are # In most cases, IFLAGS = -I../include # If loading an external FFTW library, add the location of FFTW include files IFLAGS = -I../include # MODFLAGS = flag used by f90 compiler to locate modules # You need to search for modules in ./, in ../iotk/src, in ../Modules # Some applications also neeed modules in ../PW, ../PH, ../CPV MODFLAGS = -I./ -I../Modules -I../iotk/src \ -I../PW -I../PH -I../CPV # Compilers: fortran-90, fortran-77, C # If a parallel compilation is desired, MPIF90 should be a fortran-90 # compiler that produces executables for parallel execution using MPI # (such as for instance mpif90, mpf90, mpxlf90,...); # otherwise, an ordinary fortran-90 compiler (f90, g95, xlf90, ifort,...) # If you have a parallel machine but no suitable candidate for MPIF90, # try to specify the directory containing "mpif.h" in IFLAGS # and to specify the location of MPI libraries in MPI_LIBS MPIF90 = ifort #F90 = ifort CC = cc F77 = ifort # C preprocessor and preprocessing flags - for explicit preprocessing, # if needed (see the compilation rules above) # preprocessing flags must include DFLAGS and IFLAGS CPP = cpp CPPFLAGS = -P -traditional $(DFLAGS) $(IFLAGS) # compiler flags: C, F90, F77 # C flags must include DFLAGS and IFLAGS # F90 flags must include MODFLAGS, IFLAGS, and FDFLAGS with appropriate syntax CFLAGS = -O3 $(DFLAGS) $(IFLAGS) F90FLAGS = $(FFLAGS) -nomodule -fpp $(FDFLAGS) $(IFLAGS) $(MODFLAGS) FFLAGS = -O2 -tpp6 -assume byterecl # compiler flags without optimization for fortran-77 # the latter is NEEDED to properly compile dlamch.f, used by lapack FFLAGS_NOOPT = -O0 -assume byterecl # Linker and linker-specific flags (if any) # Typically LD coincides with F90 or MPIF90 - not actually used # LD = ifort LDFLAGS = # External Libraries (if any) : blas, lapack, fft, MPI # If you have nothing better, use the local copy : ../flib/blas.a BLAS_LIBS = ../flib/blas.a # The following lapack libraries will be available in flib/ : # ../flib/lapack.a : contains all needed routines # ../flib/lapack_atlas.a: only routines not present in the Atlas library # For IBM machines with essl: load essl BEFORE lapack ! # remember that LAPACK_LIBS precedes BLAS_LIBS in loading order LAPACK_LIBS = ../flib/lapack.a # nothing needed here if the the internal copy of FFTW is compiled # (needs -D__FFTW -D__USE_INTERNAL_FFTW in DFLAGS) FFT_LIBS = # For parallel execution, the correct path to MPI libraries must # be specified in MPI_LIBS (except for IBM if you use mpxlf) MPI_LIBS = # IBM-specific: MASS libraries, if available and if -D__MASS is defined in FDFLAGS MASS_LIBS = # pgplot libraries (used by some post-processing tools) PGPLOT_LIBS = # ar command and flags - for most architectures: AR = ar, ARFLAGS = ruv # ARFLAGS_DYNAMICS is used in iotk to produce a dynamical library, # for Mac OS-X with PowerPC and xlf compiler. In all other cases # ARFLAGS_DYNAMICS = $(ARFLAGS) AR = ar ARFLAGS = ruv ARFLAGS_DYNAMIC= ruv # ranlib command. If ranlib is not needed (it isn't in most cases) use # RANLIB = echo RANLIB = ranlib # all internal and external libraries - do not modify LIBOBJS = ../flib/ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FFT_LIBS) $(MPI_LIBS) $(MASS_LIBS) $(PGPLOT_LIBS) i saw that for mpif90 and F77, ifort compiler want to use so i change all of them to mpif77. and i compiled it.by doing that i could use both of my computer's cpu but this error was hapen at the end of my runs. It seems that [at least] one of the processes that was started with mpirun did not invoke MPI_INIT before quitting (it is possible that more than one process did not invoke MPI_INIT -- mpirun was only notified of the first one, which was on node n0). mpirun can *only* be used with MPI programs (i.e., programs that invoke MPI_INIT and MPI_FINALIZE). You can use the "lamexec" program to run non-MPI programs over the lambooted nodes. ----------------------------------------------------------------------------- forrtl: error (78): process killed (SIGTERM) mpirun failed with exit status 252 my computer run both of cpus but he didn't share kpoint he only do the same job with both cpus. please help me i really confused why it happended. sincerely yours On 12/2/06, Amin Babazadeh wrote: > > Dear Dr.Zhou and kohlmeyer > Thanks a lot for your helps. i will try to do your recommendation. > Sincerely yours > amin > > On 12/2/06, Huiqun Zhou < hqzhou at nju.edu.cn> wrote: > > > > Amin, > > > > Sorry, I was out of the town and had no access to my e-mail. > > > > 1. You can use anyone of MPI implemetations. But I recommend Intel MPI-2 > > because it's an > > installable binary, it saves you as a beginner a lot of time. If you > > cannot get a copy of that, > > use OpenMPI, a successor of LAM/MPI. > > 2. Basically, when you recompile MPI, you can add > > --prefix=/your/favourite/place to configure > > 3. You need C compiler to compile MPI. You need gcc too. I compiled MPI > > with icc + ifort. > > > > Good luck! > > > > Huiqun > > > > > > ----- Original Message ----- > > *From:* Amin Babazadeh > > *To:* pw_forum at pwscf.org > > *Sent:* Thursday, November 30, 2006 3:17 PM > > *Subject:* Re: [Pw_forum] use doual core > > > > > > Thanks a lot for your answers.but until yet i couldn't solve my > > problem.I confused about mpi. there are three kind of mpi in the > > Internet (lam/mpi,openmpi,mpich) i don't know which one of them i should > > install. > > about making the environment i should say that i am beginner in using > > Linux so i use the ./configure commend and i didn't change any path because > > i don't know how i should do it. > > i will appreciate if answer my question? > > 1-which mpi do i need for my job? > > 2-how could i change the path? > > 3-is ifort compiler enough for installing mpi package? > > Thanks a lot > > > > On 11/27/06, Huiqun Zhou wrote: > > > > > > Have you set up you environment for using one the mpi libraries you > > > installed in .bashrc? > > > For example, for openmpi you need to set following in your .bashrc if > > > you are using bash > > > as your shell: > > > ... > > > export PATH=/opt/openmpi/bin:$PATH > > > export LD_LIBRARY_PATH=/opt/openmpi/lib:$LD_LIBRARY_PATH > > > ... > > > > > > Note: you need to replace /opt/openmpi with the path of your > > > installation. > > > > > > Huiqun Zhou > > > > > > > > > ----- Original Message ----- > > > *From:* Amin Babazadeh > > > *To:* pw_forum at pwscf.org > > > *Sent:* Sunday, November 26, 2006 6:11 PM > > > *Subject:* Re: [Pw_forum] use doual core > > > > > > > > > Dear Dr.Kohlmeyer > > > Thanks a lot for your help.I did what you said.i installed > > > fftw-3.1.2.tar > > > lam-7.1.2.tar > > > mpich2-1.0.4p1.tar > > > openmpi-1.1.2.tar > > > on fedora core 5 and after that i configure the espresso but > > > this error was written > > > > > > WARNING: the following problems were detected: > > > > > > unsupported C/Fortran compilers combination: > > > CC=mpicc, F77=mpif77, F90=mpif90 > > > you may not be able to compile this program. > > > i don't know what this problem means.would you please help me. > > > Thanks a lot > > > > > > > > > > > > On 11/22/06, Axel Kohlmeyer wrote: > > > > > > > > On 11/22/06, Amin Babazadeh < babazade at gmail.com> wrote: > > > > > dear users > > > > > I use a computer with a dual core CPU.but my problem is that when > > > > i run a > > > > > program only one of the CPU work but i like to share the work > > > > (solving k > > > > > points) between cpus. > > > > > I think that i should install the parallel pwscf but when i run > > > > the > > > > > ./configure only single pwscf installed. > > > > > > > > you have to install an MPI package (e.g. LAM/MPI, OpenMPI, MPICH) > > > > first and then configure/compile quantum espresso with parallel > > > > support > > > > as explained in the provided installation instructions. > > > > > > > > please make sure that your MPI package is compatible with or > > > > compiled > > > > for the fortran compiler you want to use to compiled quantum > > > > espresso with. > > > > precompiled packages may be compiled for a different compiler and > > > > thus > > > > need special flags or environment variables set to use the compiler > > > > of > > > > your choice. > > > > > > > > axel. > > > > > > > > > would you please tell me or give me a document that solve my > > > > problem. > > > > > > > > > > > > > > > -- > > > > > AMIN > > > > > > > > > > > > -- > > > > > > > > ======================================================================= > > > > 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 > > > > > > > > > > > > > > > > -- > > > AMIN > > > > > > > > > > > > -- > > AMIN > > > > > > > -- > AMIN -- AMIN -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061210/c1b78e5f/attachment.htm From babazade at gmail.com Sun Dec 10 15:11:40 2006 From: babazade at gmail.com (Amin Babazadeh) Date: Sun, 10 Dec 2006 17:41:40 +0330 Subject: [Pw_forum] problem with k-points In-Reply-To: <20061209044431.6599.qmail@webmail54.rediffmail.com> References: <20061209044431.6599.qmail@webmail54.rediffmail.com> Message-ID: Dear sanjeev On 9 Dec 2006 04:44:31 -0000, Sanjeev Kumar Gupta < sanjeev0302 at rediffmail.com> wrote: > > Respected sir, > > i am sanjeev gupta, from india, working DFT calculation via > Quantum-Espresso-3.1.1. I have doubts with k-ponits, > 1)How we choose k-points for diiferent system? > dis is done in espresso code automatically for scf and nscf but for plotting band structure you should do it manually 2)Is possible fermi energy negative for noble nitrides? > I thought it is possible.negative or positive Fermi energy doesn't have physical meaning. 3)Is neccessary same k-points for scf and nscf cycle or phX,phL and phG.? > no you can change it.for scf and nscf.usually the kpoint for scf > calculation is smaller than nscf.about phX,phL and phG i don't have any > idea. > good luck amin with regards > sanjeev gupta > > ==================================================== > Sanjeev Kumar Gupta > Junior Research Fellow (DAE-BRNS) > Computational Condensed Matter Physics Lab.(CCMP) > Department of Physics, Faculty of Science, > The M.S.University of Baroda, Vadodara - 390 002. > Ph.No: +91-265-279 5339 (O) extn: 30-25 > mobile:09374616019 > Email: sanjeev0302 at rediffmail.com > sanjeev0302 at yahoo.co.in > skgupta-phy at msubaroda.ac.in > ==================================================== > > Residential Address- > > Dr. Vikram Sarabhai Hall, > Room No.-95, Boys' Hostel,M.S.University Campus, > Pratapgunj,Vadodara-390 002,Gujarat,INDIA > > > > -- AMIN -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061210/b7908701/attachment.htm From baroni at sissa.it Sun Dec 10 16:07:11 2006 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 10 Dec 2006 16:07:11 +0100 Subject: [Pw_forum] phonon calc. for fcc at X In-Reply-To: <175910.68037.qm@web34802.mail.mud.yahoo.com> References: <175910.68037.qm@web34802.mail.mud.yahoo.com> Message-ID: <0C0EB125-858C-4123-8E78-98F7C7D09C03@sissa.it> Dear Emin, dear all: all my apologies! Nicola was of course right, and I was WRONG! (011) IS indeed equivalent to (001), because the latter is equivalent to (-1,0,0) and the difference between (011) and (-100) is (111) which IS an FCC reciprocal-lattice vector. The coordinates of the K point are (3/4,3/4,0). With reference to the figure mentioned in the link below, K is the intersection among the planes x+y+z=3/2, z=0, and x=y, hence the above coordinates. To come to your original question. Are the symmetries/degeneracies of the results what you expect? Can you make the input/output of your calculation accessible to us? Stefano On Dec 10, 2006, at 2:46 PM, e kb wrote: > Thank you for your answer Stefano, > Of course this explains the different frequencies, > and that also means that I misunderstand the kpoints given in > example 5, > about band structure for an fcc, > and Dr. Marzari's explanation to another QE user, > who was confused like me. > http://www.democritos.it/pipermail/pw_forum/2006-June/004365.html > > Thank you again, > Emine Kucukbenli > > Stefano Baroni wrote: > Emine: (001) and (011) are *NOT* two "X" points in the FCC > Brillouin zone. The difference between the second and the first > (010) is *NOT* a reciprocal-space vector. If it was, X would also > be, which you will agree it is not. As a matter of fact, (011) has > its own nickname (it is called "K"). No surprise, therefore, that > frequencies @K are different from frequencies @X. Are these > arguments clear and convincing enough? Stefano > > > On Dec 9, 2006, at 11:10 PM, e kb wrote: > >> Dear QE users, >> I am performing phonon calculations for a zinc blende structure, >> I calculated the frequencies at high symmetry points, evaluating a >> single point at each time. >> So I followed the procedure of scf, nscf and ph.x calculation one >> by one for L(0.5 0.5 0.5) - Gamma - X(0,0,1) - X(0,1,1) points. >> In these calculations every parameter (else than q-vector in >> &phonon list in nscf calculation and phonon card for ph.x input of >> course) is kept fixed. >> >> Although I expect the frequencies at two X points - (0,0,1) and >> (0,1,1) - to be the same, >> the difference in TA modes' frequencies are around 30 cm-1, >> in the other ones, around 5 cm-1. >> >> I would like to attribute this to unconverged lattice parameters, >> cut off energies or thresholds etc. but what I do not understand >> is why the program treats these two points differently, although >> they should be equivalent. So I expect to see the same value for >> frequency at these points, even if it is wrong, highly negative, >> or sth else that it should not be. >> >> I will appreciate any answers. >> Thank you. >> >> Emine Kucukbenli >> >> >> >> Everyone is raving about the all-new Yahoo! Mail beta. > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - > Trieste > [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > Check out the all-new Yahoo! Mail beta - Fire up a more powerful > email and get things done faster. --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061210/20d62319/attachment.htm From sanjeev0302 at rediffmail.com Sun Dec 10 17:20:15 2006 From: sanjeev0302 at rediffmail.com (Sanjeev Kumar Gupta) Date: 10 Dec 2006 16:20:15 -0000 Subject: [Pw_forum] problem with k-points Message-ID: <20061210162015.13029.qmail@webmail58.rediffmail.com> Thanking you Amin, >>This is done in espresso code automatically for scf and nscf but for plotting band structure you should do it manually>> But what will be the maximum and minimum range of the k-point for band calculation and also you said in earlier suggestion that, for scf and nscf it is automatic,but we want to do manually the how we will proceeds? >>I thought it is possible.negative or positive Fermi energy doesn't have physical meaning>> sorry, for again same question, what is significance of negative fermi energy is any relation in other calculation. I want to find out the elastic constant for my system, how we will proceeds? Regards sanjeev On Sun, 10 Dec 2006 Amin Babazadeh wrote : >Dear sanjeev > > > >On 9 Dec 2006 04:44:31 -0000, Sanjeev Kumar Gupta < >sanjeev0302 at rediffmail.com> wrote: >> >>Respected sir, >> >>i am sanjeev gupta, from india, working DFT calculation via >>Quantum-Espresso-3.1.1. I have doubts with k-ponits, >>1)How we choose k-points for diiferent system? >> > >dis is done in espresso code automatically for scf and nscf but for plotting >band structure you should do it manually > >2)Is possible fermi energy negative for noble nitrides? >> >. > > >3)Is neccessary same k-points for scf and nscf cycle or phX,phL and phG.? >>no you can change it.for scf and nscf.usually the kpoint for scf >>calculation is smaller than nscf.about phX,phL and phG i don't have any >>idea. >> > >good luck >amin > >with regards >>sanjeev gupta >> >>==================================================== >>Sanjeev Kumar Gupta >>Junior Research Fellow (DAE-BRNS) >>Computational Condensed Matter Physics Lab.(CCMP) >>Department of Physics, Faculty of Science, >>The M.S.University of Baroda, Vadodara - 390 002. >>Ph.No: +91-265-279 5339 (O) extn: 30-25 >>mobile:09374616019 >>Email: sanjeev0302 at rediffmail.com >> sanjeev0302 at yahoo.co.in >> skgupta-phy at msubaroda.ac.in >>==================================================== >> >>Residential Address- >> >>Dr. Vikram Sarabhai Hall, >>Room No.-95, Boys' Hostel,M.S.University Campus, >>Pratapgunj,Vadodara-390 002,Gujarat,INDIA >> >> >> >> > > > > >-- AMIN ==================================================== Sanjeev Kumar Gupta Junior Research Fellow (DAE-BRNS) Computational Condensed Matter Physics Lab.(CCMP) Department of Physics, Faculty of Science, The M.S.University of Baroda, Vadodara - 390 002. Ph.No: +91-265-279 5339 (O) extn: 30-25 mobile:09374616019 Email: sanjeev0302 at rediffmail.com sanjeev0302 at yahoo.co.in skgupta-phy at msubaroda.ac.in ==================================================== Residential Address- Dr. Vikram Sarabhai Hall, Room No.-95, Boys' Hostel,M.S.University Campus, Pratapgunj,Vadodara-390 002,Gujarat,INDIA -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061210/1529e7fa/attachment.htm From eminekb at yahoo.com Sun Dec 10 17:57:14 2006 From: eminekb at yahoo.com (e kb) Date: Sun, 10 Dec 2006 08:57:14 -0800 (PST) Subject: [Pw_forum] phonon calc. for fcc at X In-Reply-To: <0C0EB125-858C-4123-8E78-98F7C7D09C03@sissa.it> Message-ID: <884235.52573.qm@web34814.mail.mud.yahoo.com> Dear Stefano , QE users, Thank you for your interest, Here are the scf, nscf and ph.x input files respectively, for X(0,0,1). For X(0,1,1) the scf file is the same, in nscf input I just changed the phonon namelist to (0.00 1.00 1.00) so not to make the mail longer and unreadable, I am skipping it and just adding ph.X input for X(0,1,1). I should note that this was a part of test calculations for the new pseudo for Indium that I recently generated using the 'atomic' code. The cut off energy that I used for these calculations (34 Ryd) is chosen to be enough to represent correct lattice constants, but still the pseudo and the value of cut off energy needs further examination. That is why I would not be surprised to see any discrepiencies in the frequencies. But again, I could not understand the differences that occured for the same point. With a verbose output I checked the phonon polarization vectors, As far as I understand, the calculation is done for the same modes for the two points. I do not want to bother you with the whole output files, if this is a very simple problem that an experienced/careful user can notice from the inputs, otherwise I can attach the output files. Buona domenica, Emine Kucukbenli ------------ &control calculation = 'scf' restart_mode='from_scratch', prefix='34_vib', tprnfor = .true. pseudo_dir = '$PSEUDO_DIR' , etot_conv_thr = 1.0D-5 / &system ibrav= 2, celldm(1)=9.593140000 nat= 2, ntyp= 2, ecutwfc =34.0, ecutrho =272.0, occupations = 'smearing' smearing = 'gaussian' degauss = 0.004, / &electrons mixing_mode = 'plain' mixing_beta = 0.7 / ATOMIC_SPECIES In 114.818 In_us_2.upf N 14.0067 N.pbe-van_ak.UPF ATOMIC_POSITIONS { crystal } In 0.00000000000 0.00000000000 0.0000000000000 N 0.25000000000 0.25000000000 0.2500000000000 K_POINTS { automatic } 8 8 8 0 0 0 ------------ &control calculation = 'phonon' restart_mode='from_scratch', prefix='34_vib', tprnfor = .true. pseudo_dir = '$PSEUDO_DIR' , etot_conv_thr = 1.0D-5 / &system ibrav= 2, celldm(1)=9.593140000 nat= 2, ntyp= 2, ecutwfc =34.0, ecutrho =272.0, occupations = 'smearing' smearing = 'gaussian' degauss = 0.004, / &electrons mixing_mode = 'plain' mixing_beta = 0.7 / &phonon xqq(1) = .00, xqq(2) = .00, xqq(3) = 1.00 / ATOMIC_SPECIES In 114.818 In_us_2.upf N 14.0067 N.pbe-van_ak.UPF ATOMIC_POSITIONS { crystal } In 0.00000000000 0.00000000000 0.0000000000000 N 0.25000000000 0.25000000000 0.2500000000000 K_POINTS { automatic } 8 8 8 0 0 0 ------------------------- &inputph tr2_ph=1.0d-14, amass(1)=114.818, amass(2)=14.0067, prefix='34_vib', fildyn='34_vib.dyn', / 0.00 0.00 1.00 -------------------------------- &inputph tr2_ph=1.0d-14, amass(1)=114.818, amass(2)=14.0067, prefix='34_vib', fildyn='34_vib.dyn', / 0.00 1.00 1.00 ---------------------------------- X(0,0,1) omega( 1) = 3.163928 [THz] = 105.537987 [cm-1] omega( 2) = 3.163928 [THz] = 105.537987 [cm-1] omega( 3) = 6.030058 [THz] = 201.142433 [cm-1] omega( 4) = 14.775784 [THz] = 492.870383 [cm-1] omega( 5) = 14.775784 [THz] = 492.870383 [cm-1] omega( 6) = 16.372030 [THz] = 546.115769 [cm-1] X(0,1,1) omega( 1) = 2.153190 [THz] = 71.823161 [cm-1] omega( 2) = 2.153190 [THz] = 71.823161 [cm-1] omega( 3) = 6.239891 [THz] = 208.141736 [cm-1] omega( 4) = 14.879198 [THz] = 496.319913 [cm-1] omega( 5) = 14.879198 [THz] = 496.319913 [cm-1] omega( 6) = 16.354833 [THz] = 545.542147 [cm-1] ---------------------------------- Stefano Baroni wrote: Dear Emin, dear all: all my apologies! Nicola was of course right, and I was WRONG! (011) IS indeed equivalent to (001), because the latter is equivalent to (-1,0,0) and the difference between (011) and (-100) is (111) which IS an FCC reciprocal-lattice vector. The coordinates of the K point are (3/4,3/4,0). With reference to the figure mentioned in the link below, K is the intersection among the planes x+y+z=3/2, z=0, and x=y, hence the above coordinates. To come to your original question. Are the symmetries/degeneracies of the results what you expect? Can you make the input/output of your calculation accessible to us? Stefano On Dec 10, 2006, at 2:46 PM, e kb wrote: Thank you for your answer Stefano, Of course this explains the different frequencies, and that also means that I misunderstand the kpoints given in example 5, about band structure for an fcc, and Dr. Marzari's explanation to another QE user, who was confused like me. http://www.democritos.it/pipermail/pw_forum/2006-June/004365.html Thank you again, Emine Kucukbenli Stefano Baroni wrote: Emine: (001) and (011) are *NOT* two "X" points in the FCC Brillouin zone. The difference between the second and the first (010) is *NOT* a reciprocal-space vector. If it was, X would also be, which you will agree it is not. As a matter of fact, (011) has its own nickname (it is called "K"). No surprise, therefore, that frequencies @K are different from frequencies @X. Are these arguments clear and convincing enough? Stefano On Dec 9, 2006, at 11:10 PM, e kb wrote: Dear QE users, I am performing phonon calculations for a zinc blende structure, I calculated the frequencies at high symmetry points, evaluating a single point at each time. So I followed the procedure of scf, nscf and ph.x calculation one by one for L(0.5 0.5 0.5) - Gamma - X(0,0,1) - X(0,1,1) points. In these calculations every parameter (else than q-vector in &phonon list in nscf calculation and phonon card for ph.x input of course) is kept fixed. Although I expect the frequencies at two X points - (0,0,1) and (0,1,1) - to be the same, the difference in TA modes' frequencies are around 30 cm-1, in the other ones, around 5 cm-1. I would like to attribute this to unconverged lattice parameters, cut off energies or thresholds etc. but what I do not understand is why the program treats these two points differently, although they should be equivalent. So I expect to see the same value for frequency at these points, even if it is wrong, highly negative, or sth else that it should not be. I will appreciate any answers. Thank you. Emine Kucukbenli --------------------------------- Everyone is raving about the all-new Yahoo! Mail beta. --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html --------------------------------- Check out the all-new Yahoo! Mail beta - Fire up a more powerful email and get things done faster. --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html --------------------------------- Have a burning question? Go to Yahoo! Answers and get answers from real people who know. -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061210/24516b24/attachment.htm From eminekb at yahoo.com Sun Dec 10 18:27:56 2006 From: eminekb at yahoo.com (e kb) Date: Sun, 10 Dec 2006 09:27:56 -0800 (PST) Subject: [Pw_forum] problem with k-points In-Reply-To: <20061210162015.13029.qmail@webmail58.rediffmail.com> Message-ID: <885736.13583.qm@web34803.mail.mud.yahoo.com> Dear Sanjeev, I would like to say you may find example 5 useful for your questions about k points. There you can find how to enter k points manually for scf and nscf calculations. I think it is necessary to check the weight of k points for scf, but for nscf band structure calc. as in example 05 that may not have any significance, For the elastic constants, using the well known strain-stress relation and elastic energy density expression, is the first way that comes to my mind. The convention about which strain to use to obtain which elastic constant, is probably told in many references that one can check in the literature. For a simple explanation for a simple system, you can take a look at Phys. Rev. B 60, 791 - 799 (1999) and erratum. I am a new user of QE, and not even a grad student yet, so if I said sth wrong, I hope more experienced users will correct me. Bests, Emine Kucukbenli Sanjeev Kumar Gupta wrote: Thanking you Amin, >>This is done in espresso code automatically for scf and nscf but for plotting band structure you should do it manually>> But what will be the maximum and minimum range of the k-point for band calculation and also you said in earlier suggestion that, for scf and nscf it is automatic,but we want to do manually the how we will proceeds? >>I thought it is possible.negative or positive Fermi energy doesn't have physical meaning>> sorry, for again same question, what is significance of negative fermi energy is any relation in other calculation. I want to find out the elastic constant for my system, how we will proceeds? Regards sanjeev On Sun, 10 Dec 2006 Amin Babazadeh wrote : >Dear sanjeev > > > >On 9 Dec 2006 04:44:31 -0000, Sanjeev Kumar Gupta < >sanjeev0302 at rediffmail.com> wrote: >> >>Respected sir, >> >>i am sanjeev gupta, from india, working DFT calculation via >>Quantum-Espresso-3.1.1. I have doubts with k-ponits, >>1)How we choose k-points for diiferent system? >> > >dis is done in espresso code automatically for scf and nscf but for plotting >band structure you should do it manually > >2)Is possible fermi energy negative for noble nitrides? >> >. > > >3)Is neccessary same k-points for scf and nscf cycle or phX,phL and phG.? >>no you can change it.for scf and nscf.usually the kpoint for scf >>calculation is smaller than nscf.about phX,phL and phG i don't have any >>idea. >> > >good luck >amin > >with regards >>sanjeev gupta >> >>==================================================== >>Sanjeev Kumar Gupta >>Junior Research Fellow (DAE-BRNS) >>Computational Condensed Matter Physics Lab.(CCMP) >>Department of Physics, Faculty of Science, >>The M.S.University of Baroda, Vadodara - 390 002. >>Ph.No: +91-265-279 5339 (O) extn: 30-25 >>mobile:09374616019 >>Email: sanjeev0302 at rediffmail.com >> sanjeev0302 at yahoo.co.in >> skgupta-phy at msubaroda.ac.in >>==================================================== >> >>Residential Address- >> >>Dr. Vikram Sarabhai Hall, >>Room No.-95, Boys' Hostel,M.S.University Campus, >>Pratapgunj,Vadodara-390 002,Gujarat,INDIA >> >> >> >> > > > > >-- AMIN ==================================================== Sanjeev Kumar Gupta Junior Research Fellow (DAE-BRNS) Computational Condensed Matter Physics Lab.(CCMP) Department of Physics, Faculty of Science, The M.S.University of Baroda, Vadodara - 390 002. Ph.No: +91-265-279 5339 (O) extn: 30-25 mobile:09374616019 Email: sanjeev0302 at rediffmail.com sanjeev0302 at yahoo.co.in skgupta-phy at msubaroda.ac.in ==================================================== Residential Address- Dr. Vikram Sarabhai Hall, Room No.-95, Boys' Hostel,M.S.University Campus, Pratapgunj,Vadodara-390 002,Gujarat,INDIA --------------------------------- Need a quick answer? Get one in minutes from people who know. Ask your question on Yahoo! Answers. -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061210/630acef1/attachment.htm From degironc at sissa.it Sun Dec 10 23:34:55 2006 From: degironc at sissa.it (Stefano de Gironcoli) Date: Sun, 10 Dec 2006 23:34:55 +0100 (CET) Subject: [Pw_forum] phonon calc. for fcc at X In-Reply-To: <884235.52573.qm@web34814.mail.mud.yahoo.com> References: <884235.52573.qm@web34814.mail.mud.yahoo.com> Message-ID: If I remember correctly there used to be a term in the phonon calculation in which the perturbing potential was written as DeltaV(r) = exp(+iqr)*\DeltaVperiodic(r) and \DeltaVperiodic was expanded up to the charge density cutoff ... this term was therefore slightly different for two q wavevectors that would otherwise be equivalent. This never gave any noticeable difference in real calculations and I would be surprised if this would be the cause of your results but a way to check this is to increase the charge density cutoff and see what happens as in this case the problem should disappear when the potential description become complete. From akohlmey at cmm.chem.upenn.edu Sun Dec 10 23:59:16 2006 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sun, 10 Dec 2006 17:59:16 -0500 (EST) Subject: [Pw_forum] use doual core In-Reply-To: Message-ID: On Sun, 10 Dec 2006, Amin Babazadeh wrote: dear amin, [...] AB> # See include/defs.h.README for a list of options and their meaning AB> # With the exception of IBM xlf, FDFLAGS = $(DFLAGS) AB> # For IBM xlf, FDFLAGS is the same as DFLAGS with separating commas AB> AB> DFLAGS = -D__INTEL -D__FFTW -D__USE_INTERNAL_FFTW for parallel compilation there should be a -D__PARA here. so you basically compiled the serial version (using mpif77 instead of ifort doesn't automatically mean that you compile the parallel version). so please do a 'make clean' and then re-configure with: env MPIF90=mpif77 ./configure check the output of the configure command, and then re-compile. [...] AB> my computer run both of cpus but he didn't share kpoint he only do the same AB> job with both cpus. yep. this is what is supposed to happen if you start a non-parallel program aross multiple cpus with MPI. MPI parallel programs are supposed to be independent until they call MPI_INIT and after MPI_FINALIZE. a serial program (even if compiled with an MPI compiler wrapper) does not contain these calls and hence you get the behavior you see and the warning from mpirun. if you want to learn more details about this, i recommend you look into some of the MPI tutorials on the web, that make this very clear. cheers, axel. AB> please help me i really confused why it happended. AB> sincerely yours AB> AB> [...] -- ======================================================================= 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 eminekb at yahoo.com Mon Dec 11 00:05:37 2006 From: eminekb at yahoo.com (e kb) Date: Sun, 10 Dec 2006 15:05:37 -0800 (PST) Subject: [Pw_forum] phonon calc. for fcc at X In-Reply-To: Message-ID: <560650.33393.qm@web34802.mail.mud.yahoo.com> Dear Stefano, Thank you, I will study the relevant part for pert. potential., do the suggested tests and modifications, and send the result back to close the case. But a fast point that I wanted to note that is, InN turns out to be a metal according to my calculations, without several corrections used, like GW or SIC. That was the reason of the k-mesh. Thank you for your help. Emine Kucukbenli Stefano de Gironcoli wrote: If I remember correctly there used to be a term in the phonon calculation in which the perturbing potential was written as DeltaV(r) = exp(+iqr)*\DeltaVperiodic(r) and \DeltaVperiodic was expanded up to the charge density cutoff ... this term was therefore slightly different for two q wavevectors that would otherwise be equivalent. This never gave any noticeable difference in real calculations and I would be surprised if this would be the cause of your results but a way to check this is to increase the charge density cutoff and see what happens as in this case the problem should disappear when the potential description become complete. From s305igun at mail.chem.itb.ac.id Mon Dec 11 03:37:07 2006 From: s305igun at mail.chem.itb.ac.id (Rahmat Gunawan) Date: Mon, 11 Dec 2006 09:37:07 +0700 (WIT) Subject: [Pw_forum] problem in k-points of hydrogen-graphite system In-Reply-To: References: <35689.167.205.72.2.1165679588.squirrel@webmail.chem.itb.ac.id> Message-ID: <1175.167.205.72.36.1165804627.squirrel@webmail.chem.itb.ac.id> Dear Pw_Forum Halo Axel, I would like to thanks to You and I am sorry I was forget to write my input in this forum. Now, I try post my graphite input in PWscf packege: there are 6 file input, and I do not know is it true input? and this are the six input: 1. File 1: graphite.scf.in &CONTROL calculation = 'relax' , restart_mode = 'from_scratch' , outdir = '/home/s3/s305igun/tmp/' , pseudo_dir = '/home/s3/s305igun/pseudo/' , prefix = 'graphite' , / &SYSTEM ibrav = 4, celldm(1) = 4.64117, celldm(3) = 2.7264, nat = 4, ntyp = 1, ecutwfc = 18.0, ecutrho = 300.0 , / &ELECTRONS conv_thr = 1.0d-8 mixing_beta = 0.7 / &IONS pot_extrapolation = "second_order", wfc_extrapolation = "second_order", / ATOMIC_SPECIES C 12.01100 C.pz-vbc.UPF ATOMIC_POSITIONS crystal C 0.000000000 0.000000000 0.000000000 C 0.333333333 0.666666666 0.000000000 C 0.000000000 0.000000000 0.500000000 C 0.666666666 0.333333333 0.500000000 K_POINTS { automatic } 4 4 1 0 0 0 2. File 2: graphite.pp.rho.in &inputpp prefix = 'graphite' outdir = '/home/s3/s305igun/tmp/' filplot = 'graphitecharge' plot_num= 0 / &plot nfile = 1 filepp(1) = 'graphitecharge' weight(1) = 1.0 iflag = 2 output_format = 2 fileout = 'graphite.rho.dat' e1(1) =1.0, e1(2)=1.0, e1(3) = 0.0, e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0, nx=56, ny=40 / 3. File 3: graphite.plotrho.in graphite.rho.dat graphite.rho.ps n 0 0.09 6 4. File 4: graphite.band.in &CONTROL calculation = 'nscf' , restart_mode = 'from_scratch' , outdir = '/home/s3/s305igun/tmp/' , pseudo_dir = '/home/s3/s305igun/pseudo/' , prefix = 'graphite' , / &SYSTEM ibrav = 4, celldm(1) = 4.64117, celldm(3) = 2.7264, nat = 4, ntyp = 1, ecutwfc = 18.0, ecutrho = 300.0 , / &ELECTRONS conv_thr = 1.0d-8 mixing_beta = 0.7 / ATOMIC_SPECIES C 12.01100 C.pz-vbc.UPF ATOMIC_POSITIONS crystal C 0.000000000 0.000000000 0.000000000 C 0.333333333 0.666666666 0.000000000 C 0.000000000 0.000000000 0.500000000 C 0.666666666 0.333333333 0.500000000 K_POINTS tpiba 28 0.0000000 0.0000000 0.0000000 0.0100000 0.0000000 0.0000000 -0.0867450 0.0100000 0.0000000 0.1154701 0.0000000 0.0600000 0.0000000 0.1154701 -0.0867450 0.0600000 0.0000000 0.2309401 0.0000000 0.0600000 0.0000000 0.2309401 -0.0867450 0.0600000 0.0000000 0.3464102 0.0000000 0.0600000 0.0000000 0.3464102 -0.0867450 0.0600000 0.0000000 0.4618802 0.0000000 0.0600000 0.0000000 0.4618802 -0.0867450 0.0600000 0.0000000 -0.5773503 0.0000000 0.0300000 0.0000000 -0.5773503 -0.0867450 0.0300000 0.1000000 0.1732051 0.0000000 0.0600000 0.1000000 0.1732051 -0.0867450 0.0600000 0.1000000 0.2886751 0.0000000 0.1200000 0.1000000 0.2886751 -0.0867450 0.1200000 0.1000000 0.4041452 0.0000000 0.1200000 0.1000000 0.4041452 -0.0867450 0.1200000 0.1000000 0.5196152 0.0000000 0.1200000 0.1000000 0.5196152 -0.0867450 0.1200000 0.2000000 0.3464102 0.0000000 0.0600000 0.2000000 0.3464102 -0.0867450 0.0600000 0.2000000 0.4618802 0.0000000 0.1200000 0.2000000 0.4618802 -0.0867450 0.1200000 0.2000000 0.5773503 0.0000000 0.0600000 0.2000000 0.5773503 -0.0867450 0.0600000 0.3000000 0.5196152 0.0000000 0.0600000 0.3000000 0.5196152 -0.0867450 0.0600000 5. File 5: graphite.bands.in &inputpp prefix = 'graphite' outdir = '/home/s3/s305igun/tmp/' filband = 'graphitebands.dat' / 6. File 6: graphite.plotband.in graphitebands.dat -6.0 10 graphitebands.xmgr graphitebands.ps 6.255 1.0 6.255 oke Axel thanks for your suggest, I would like to hope your help in this forum Thanks again Success for PWscf user's research Sincerely Yours Rahmat Gunawan PostGraduate students Lab of Theoretical Chemistry Dept. of Chemistry Bandung Institute of Technology Indonesia ************************************************************************* > On Sat, 9 Dec 2006, Rahmat Gunawan wrote: > > RG> Dear PW_Forum > > RG> I would like to thank to Pw_forum, but I still have problem in our > input, > RG> so our output via ghostview (graphitebands.ps) is not good. > > please explain in which way you deem the results to be not good. > > RG> Would You like to teach us, how to write good input k-point of > graphite > RG> and hydrogen-graphite system (crystal, ibrav=4, number k-points > RG> {crystal})? > > please post an input example and explain what you want to achieve. > none of us here can see what you have tried and why you think it > may have failed. > > RG> Please help us.. > > please help _us_ to help you. > > cheers, > axel. > > RG> > RG> Thanks very much, success for your excellent research project > RG> > RG> Sincerely yours > RG> > RG> Rahmat Gunawan > RG> PostGraduate students > RG> Lab of Theoretical Chemistry > RG> Dept. of Chemistry > RG> Bandung Institute of Technology > RG> Indonesia > RG> _______________________________________________ > RG> Pw_forum mailing list > RG> Pw_forum at pwscf.org > RG> http://www.democritos.it/mailman/listinfo/pw_forum > RG> > > -- > ======================================================================= > 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 hqzhou at nju.edu.cn Mon Dec 11 03:47:54 2006 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Mon, 11 Dec 2006 10:47:54 +0800 Subject: [Pw_forum] use doual core References: <7b6913e90611220734s15038d2ei36e1e7a28166f146@mail.gmail.com> <002e01c71207$5e733cb0$1d00a8c0@solarflare> <005f01c715ed$4104e220$1d00a8c0@solarflare> Message-ID: <004601c71cce$c1a8bbd0$1d00a8c0@solarflare> Amin, In addition to Axel's suggustions, you may need to add -D__MPI option too. Huiqun ----- Original Message ----- From: Amin Babazadeh To: pw_forum at pwscf.org Sent: Sunday, December 10, 2006 10:04 PM Subject: Re: [Pw_forum] use doual core Dear friends I am so sorry for this but i couldn't solve my problem. i installed lam 7.1.2 in my computer and i didn't change the installation PATH. after that i configure the espresso.this file has been made. # make.sys. Generated from make.sys.in by configure. # compilation rules .SUFFIXES : .SUFFIXES : .o .c .f .f90 # most fortran compilers can directly preprocess c-like directives: use # $(MPIF90) $(F90FLAGS) -c $< # if explicit preprocessing by the C preprocessor is needed, use: # $(CPP) $(CPPFLAGS) $< -o $*.F90 # $(MPIF90) $(F90FLAGS) -c $*.F90 -o $*.o # remember the tabulator in the first column !!! .f90.o: $(MPIF90) $(F90FLAGS) -c $< # .f.o and .c.o: do not modify .f.o: $(F77) $(FFLAGS) -c $< .c.o: $(CC) $(CFLAGS) -c $< # DFLAGS = precompilation options (possible arguments to -D and -U) # used by the C compiler and preprocessor # FDFLAGS = as DFLAGS, for the f90 compiler # See include/defs.h.README for a list of options and their meaning # With the exception of IBM xlf, FDFLAGS = $(DFLAGS) # For IBM xlf, FDFLAGS is the same as DFLAGS with separating commas DFLAGS = -D__INTEL -D__FFTW -D__USE_INTERNAL_FFTW FDFLAGS = $(DFLAGS) # IFLAGS = how to locate directories where files to be included are # In most cases, IFLAGS = -I../include # If loading an external FFTW library, add the location of FFTW include files IFLAGS = -I../include # MODFLAGS = flag used by f90 compiler to locate modules # You need to search for modules in ./, in ../iotk/src, in ../Modules # Some applications also neeed modules in ../PW, ../PH, ../CPV MODFLAGS = -I./ -I../Modules -I../iotk/src \ -I../PW -I../PH -I../CPV # Compilers: fortran-90, fortran-77, C # If a parallel compilation is desired, MPIF90 should be a fortran-90 # compiler that produces executables for parallel execution using MPI # (such as for instance mpif90, mpf90, mpxlf90,...); # otherwise, an ordinary fortran-90 compiler (f90, g95, xlf90, ifort,...) # If you have a parallel machine but no suitable candidate for MPIF90, # try to specify the directory containing "mpif.h" in IFLAGS # and to specify the location of MPI libraries in MPI_LIBS MPIF90 = ifort #F90 = ifort CC = cc F77 = ifort # C preprocessor and preprocessing flags - for explicit preprocessing, # if needed (see the compilation rules above) # preprocessing flags must include DFLAGS and IFLAGS CPP = cpp CPPFLAGS = -P -traditional $(DFLAGS) $(IFLAGS) # compiler flags: C, F90, F77 # C flags must include DFLAGS and IFLAGS # F90 flags must include MODFLAGS, IFLAGS, and FDFLAGS with appropriate syntax CFLAGS = -O3 $(DFLAGS) $(IFLAGS) F90FLAGS = $(FFLAGS) -nomodule -fpp $(FDFLAGS) $(IFLAGS) $(MODFLAGS) FFLAGS = -O2 -tpp6 -assume byterecl # compiler flags without optimization for fortran-77 # the latter is NEEDED to properly compile dlamch.f, used by lapack FFLAGS_NOOPT = -O0 -assume byterecl # Linker and linker-specific flags (if any) # Typically LD coincides with F90 or MPIF90 - not actually used # LD = ifort LDFLAGS = # External Libraries (if any) : blas, lapack, fft, MPI # If you have nothing better, use the local copy : ../flib/blas.a BLAS_LIBS = ../flib/blas.a # The following lapack libraries will be available in flib/ : # ../flib/lapack.a : contains all needed routines # ../flib/lapack_atlas.a: only routines not present in the Atlas library # For IBM machines with essl: load essl BEFORE lapack ! # remember that LAPACK_LIBS precedes BLAS_LIBS in loading order LAPACK_LIBS = ../flib/lapack.a # nothing needed here if the the internal copy of FFTW is compiled # (needs -D__FFTW -D__USE_INTERNAL_FFTW in DFLAGS) FFT_LIBS = # For parallel execution, the correct path to MPI libraries must # be specified in MPI_LIBS (except for IBM if you use mpxlf) MPI_LIBS = # IBM-specific: MASS libraries, if available and if -D__MASS is defined in FDFLAGS MASS_LIBS = # pgplot libraries (used by some post-processing tools) PGPLOT_LIBS = # ar command and flags - for most architectures: AR = ar, ARFLAGS = ruv # ARFLAGS_DYNAMICS is used in iotk to produce a dynamical library, # for Mac OS-X with PowerPC and xlf compiler. In all other cases # ARFLAGS_DYNAMICS = $(ARFLAGS) AR = ar ARFLAGS = ruv ARFLAGS_DYNAMIC= ruv # ranlib command. If ranlib is not needed (it isn't in most cases) use # RANLIB = echo RANLIB = ranlib # all internal and external libraries - do not modify LIBOBJS = ../flib/ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FFT_LIBS) $(MPI_LIBS) $(MASS_LIBS) $(PGPLOT_LIBS) i saw that for mpif90 and F77, ifort compiler want to use so i change all of them to mpif77. and i compiled it.by doing that i could use both of my computer's cpu but this error was hapen at the end of my runs. It seems that [at least] one of the processes that was started with mpirun did not invoke MPI_INIT before quitting (it is possible that more than one process did not invoke MPI_INIT -- mpirun was only notified of the first one, which was on node n0). mpirun can *only* be used with MPI programs (i.e., programs that invoke MPI_INIT and MPI_FINALIZE). You can use the "lamexec" program to run non-MPI programs over the lambooted nodes. ----------------------------------------------------------------------------- forrtl: error (78): process killed (SIGTERM) mpirun failed with exit status 252 my computer run both of cpus but he didn't share kpoint he only do the same job with both cpus. please help me i really confused why it happended. sincerely yours On 12/2/06, Amin Babazadeh wrote: Dear Dr.Zhou and kohlmeyer Thanks a lot for your helps. i will try to do your recommendation. Sincerely yours amin On 12/2/06, Huiqun Zhou < hqzhou at nju.edu.cn> wrote: Amin, Sorry, I was out of the town and had no access to my e-mail. 1. You can use anyone of MPI implemetations. But I recommend Intel MPI-2 because it's an installable binary, it saves you as a beginner a lot of time. If you cannot get a copy of that, use OpenMPI, a successor of LAM/MPI. 2. Basically, when you recompile MPI, you can add --prefix=/your/favourite/place to configure 3. You need C compiler to compile MPI. You need gcc too. I compiled MPI with icc + ifort. Good luck! Huiqun ----- Original Message ----- From: Amin Babazadeh To: pw_forum at pwscf.org Sent: Thursday, November 30, 2006 3:17 PM Subject: Re: [Pw_forum] use doual core Thanks a lot for your answers.but until yet i couldn't solve my problem.I confused about mpi. there are three kind of mpi in the Internet (lam/mpi,openmpi,mpich) i don't know which one of them i should install. about making the environment i should say that i am beginner in using Linux so i use the ./configure commend and i didn't change any path because i don't know how i should do it. i will appreciate if answer my question? 1-which mpi do i need for my job? 2-how could i change the path? 3-is ifort compiler enough for installing mpi package? Thanks a lot On 11/27/06, Huiqun Zhou wrote: Have you set up you environment for using one the mpi libraries you installed in .bashrc? For example, for openmpi you need to set following in your .bashrc if you are using bash as your shell: ... export PATH=/opt/openmpi/bin:$PATH export LD_LIBRARY_PATH=/opt/openmpi/lib:$LD_LIBRARY_PATH ... Note: you need to replace /opt/openmpi with the path of your installation. Huiqun Zhou ----- Original Message ----- From: Amin Babazadeh To: pw_forum at pwscf.org Sent: Sunday, November 26, 2006 6:11 PM Subject: Re: [Pw_forum] use doual core Dear Dr.Kohlmeyer Thanks a lot for your help.I did what you said.i installed fftw-3.1.2.tar lam-7.1.2.tar mpich2-1.0.4p1.tar openmpi-1.1.2.tar on fedora core 5 and after that i configure the espresso but this error was written WARNING: the following problems were detected: unsupported C/Fortran compilers combination: CC=mpicc, F77=mpif77, F90=mpif90 you may not be able to compile this program. i don't know what this problem means.would you please help me. Thanks a lot On 11/22/06, Axel Kohlmeyer wrote: On 11/22/06, Amin Babazadeh < babazade at gmail.com> wrote: > dear users > I use a computer with a dual core CPU.but my problem is that when i run a > program only one of the CPU work but i like to share the work (solving k > points) between cpus. > I think that i should install the parallel pwscf but when i run the > ./configure only single pwscf installed. you have to install an MPI package (e.g. LAM/MPI, OpenMPI, MPICH) first and then configure/compile quantum espresso with parallel support as explained in the provided installation instructions. please make sure that your MPI package is compatible with or compiled for the fortran compiler you want to use to compiled quantum espresso with. precompiled packages may be compiled for a different compiler and thus need special flags or environment variables set to use the compiler of your choice. axel. > would you please tell me or give me a document that solve my problem. > > > -- > AMIN -- ======================================================================= 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 -- AMIN -- AMIN -- AMIN -- AMIN -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061211/fbcc9873/attachment.htm From amit76.india at gmail.com Mon Dec 11 05:44:13 2006 From: amit76.india at gmail.com (Amit Kumar) Date: Mon, 11 Dec 2006 10:14:13 +0530 Subject: [Pw_forum] El-ph and spin not implemented Message-ID: Dear User, I'm getting the following error for an AFM metal. from phq_readin : error # 1 El-ph and spin not implemented %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... My questions is, in the new version of pwscf is it implemented???? It would be better if you add a page in new user guide describing what's new in the current version compare to the previous versions. I have one more question:::: Why I'm not finding the executable LAMBDA.X in the executable directory of PWSCF after compilation??? Is my compilation or rather installation of pwscf not complete? Even I did not get any sample example where lambda.x has been used or any sample input file to execute lambda.x. I'll be highly obliged if you kindly give me some useful informations about the post processing of electron phonon calculation. Regards, Amit -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061211/42126bd3/attachment.htm From akohlmey at cmm.chem.upenn.edu Thu Dec 7 04:03:34 2006 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 6 Dec 2006 22:03:34 -0500 (EST) Subject: [Pw_forum] Magnetic moment on each atom In-Reply-To: <9d7293e10612061655l2dd72da8o17755d5118d24ae1@mail.gmail.com> Message-ID: On Wed, 6 Dec 2006, Jess Kondor wrote: JK> Hello, everyone JK> JK> I am studying the magnetic systems. The code (pwscf) prints absolute and JK> total magnetization. Is there a way to get the magnetic moment of each atom JK> in the unit cell? please see the previous mail about 'local' dipolar moments in extended systems. as such you only calculate the wavefunction for the whole system. the very nature of quantum mechanics is that you cannot put labels on an electrons and attribute them to individual atoms. however in principle you should something along the lines of what you want by partitioning your wavefunction/density around your atoms and then integrating over each segment (and comparing) the different results for the alpha and beta (spin) wavefunction. the tricky part is how to partition the wavefunction. of course, you'd first have to write a bit of code to do that, but it should not be tooo difficult... axel. JK> JK> Thanks, JK> JK JK> -- ======================================================================= 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 jhashemifar at gmail.com Mon Dec 11 10:55:01 2006 From: jhashemifar at gmail.com (Javad hashemifar) Date: Mon, 11 Dec 2006 10:55:01 +0100 Subject: [Pw_forum] necessare files for restart Message-ID: <2fb18d9f0612110155l74825ae4qb9347b4d92472979@mail.gmail.com> Dear Pwscf users, I have a (rather elementary) question about file management in Pwscf. Based on the following explanation (presented in /Doc/INPUT_PW): wfcdir CHARACTER ( by default same as outdir ) this directory specifies where to store files generated by each processor (*.wfc{N}, *.igk{N}, etc.). The idea here is to be able to separately store the largest files, while the files necessary for restarting still go into 'outdir' (for now only works for stand alone PW ) I assume that *.wfc{N} files are not required for restarting a converged results. But when I tested this assumption by deleting the *.wfc file of a converged system and tried to continue it one more iteration (restart_mode= restart), the program got the following error: ################################################################### # UNRECOVERABLE ERROR (ierr=1) # ERROR IN: iotk_getline (iotk_scan.spp:791) # CVS Revision: 1.3 iostat=-1 # ERROR IN: iotk_scan_tag (iotk_scan.spp:554) # CVS Revision: 1.3 # ERROR IN: iotk_scan (iotk_scan.spp:669) # CVS Revision: 1.3 # ERROR IN: iotk_scan_begin (iotk_scan.spp:98) # CVS Revision: 1.3 # namel=WFC.1 ################################################################### [0] MPI Abort by user Aborting program ! [0] Aborting program! p0_18843: p4_error: : 1 Please explain which minimum set of files are necessary for recovering a converged results by one more iteration execution. thanks in advance Javad Hashemifar ====================================== Seyed Javad Hashemifar, Ph.D. [current:] Tel:+49-203-3794743 Fax:+49-203-3794742 Fachbereich Physik (AG Kratzer), Universitat Duisburg-Essen 47048 Dusiburg, Germany [permanent:] Tel: +98-311-3912375 Fax: +98-311-3912376 Physics Department, Isfahan University of Technology 84156 Isfahan, Iran --------------------------------------------------------------------------- From giannozz at nest.sns.it Mon Dec 11 11:35:36 2006 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 11 Dec 2006 11:35:36 +0100 Subject: [Pw_forum] necessare files for restart In-Reply-To: <2fb18d9f0612110155l74825ae4qb9347b4d92472979@mail.gmail.com> References: <2fb18d9f0612110155l74825ae4qb9347b4d92472979@mail.gmail.com> Message-ID: On Dec 11, 2006, at 10:55 , Javad hashemifar wrote: > wfcdir CHARACTER ( by default same as outdir ) > this directory specifies where to store files > generated by > each processor (*.wfc{N}, *.igk{N}, etc.). The idea > here is > to be able to separately store the largest files, while > the files necessary for restarting still go into > 'outdir' > (for now only works for stand alone PW ) > > I assume that *.wfc{N} files are not required for restarting a > converged results. there is some confusion about the meaning of "restart". A "restart" is performed from an interrupted or unconverged or MD run. It requires all files (or at last, most of them). This is what the code attempts to do with "restart_mode='restart' ". If you want to calculate the band structure, you need only the self-consistent charge density and little more, and you should not specify "restart_mode='restart' ". Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at nest.sns.it Mon Dec 11 11:41:42 2006 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 11 Dec 2006 11:41:42 +0100 Subject: [Pw_forum] problem with k-points In-Reply-To: <20061210162015.13029.qmail@webmail58.rediffmail.com> References: <20061210162015.13029.qmail@webmail58.rediffmail.com> Message-ID: <21B61F1D-3744-483B-A0A2-370C933F0787@nest.sns.it> On Dec 10, 2006, at 17:20 , Sanjeev Kumar Gupta wrote: > sorry, for again same question, what is significance of negative > fermi energy is any relation in other calculation. same question, same answer: the absolute value of the Fermi energy is arbitrary in an extended system with periodic boundary conditions (i.e. an infinite crystal), because the value of the G=0 component of the potential is arbitrary Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From akohlmey at cmm.chem.upenn.edu Thu Dec 7 03:58:17 2006 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 6 Dec 2006 21:58:17 -0500 (EST) Subject: [Pw_forum] Re: Compilation Problem In-Reply-To: Message-ID: On Thu, 7 Dec 2006, Fengjie Ma wrote: FM> Hi Paolo, FM> FM> Thanks again for your help. When I removed "ntyp => nsp," and replaced FM> "ntyp" with "nsp" in PW/read_file.f90, the compilation is ok, FM> But the fourth error appears in the last step: you have to do a 'make clean' after all changes to make.sys and similar files. the error you report usually only happens, if you did not do that. please keep in mind, that you are trying to compile the code with an non standard-conformant, outdated compiler an outdated MKL library and probably with an outdated OS. even if you get the code compiled, i would _highly_ recommend to check _very_ carefully whether you get correct results. installing the current intel itanium compiler would have been _much_ less trouble... axel. FM> FM> mpif90 -o pw.x \ pwscf.o ../Modules/atom.o ../Modules/autopilot.o FM> ../Modules/basic_algebra_routines.o ../Modules/berry_phase.o FM> ../Modules/bfgs_module.o ../Modules/cell_base.o ../Modules/check_stop.o FM> ../Modules/clocks.o ../Modules/constants.o ../Modules/constraints_module.o FM> ../Modules/control_flags.o ../Modules/electrons_base.o ../Modules/fft_base.o FM> ../Modules/fft_scalar.o ../Modules/fft_types.o ../Modules/functionals.o FM> ../Modules/input_parameters.o ../Modules/io_files.o ../Modules/io_global.o FM> ../Modules/ions_base.o ../Modules/ions_nose.o ../Modules/kind.o FM> ../Modules/mp_global.o ../Modules/mp_wave.o ../Modules/mp.o FM> ../Modules/metadyn_base.o ../Modules/metadyn_io.o ../Modules/metadyn_vars.o FM> ../Modules/path_base.o ../Modules/path_formats.o ../Modules/path_variables.o FM> ../Modules/path_opt_routines.o ../Modules/path_io_routines.o FM> ../Modules/path_reparametrisation.o ../Modules/parallel_include.o FM> ../Modules/parameters.o ../Modules/parser.o ../Modules/printout_base.o FM> ../Modules/pseudo_types.o ../Modules/ptoolkit.o ../Modules/random_numbers.o FM> ../Modules/read_cards.o ../Modules/read_namelists.o ../Modules/read_upf.o FM> ../Modules/read_uspp.o ../Modules/recvec.o ../Modules/shmem_include.o FM> ../Modules/splinelib.o ../Modules/stick_base.o ../Modules/task_groups.o FM> ../Modules/timestep.o ../Modules/uspp.o ../Modules/version.o FM> ../Modules/wavefunctions.o ../Modules/wave_base.o ../Modules/xml_io_base.o FM> libpw.a ../flib/ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a FM> -lmkl_lapack -L/soft/mkl61/lib/64/ -lmkl_ipf -lguide -lpthread FM> -L/soft/mpi_intel/lib/ -lmpif90 -lmpi -lfmpi FM> ld: Warning: size of symbol `MODULE$control_flags_1' changed from 196 to 492 FM> in ../Modules/control_flags.o FM> ld: Warning: size of symbol `MODULE$reciprocal_vectors_1' changed from 352 FM> to 1016 in ../Modules/recvec.o FM> ../Modules/berry_phase.o: In function `berry_phase$$ln_setup_': FM> ../Modules/berry_phase.o(.text+0xd2): undefined reference to `ln_alloc_' FM> ../Modules/berry_phase.o(.text+0x212): undefined reference to `ln_set_' FM> ../Modules/berry_phase.o(.text+0x232): undefined reference to `ln_activate_' FM> ../Modules/berry_phase.o: In function `berry_phase$$ln_closeup_': FM> ../Modules/berry_phase.o(.text+0x322): undefined reference to `ln_dealloc_' FM> ../Modules/berry_phase.o: In function `berry_phase$$indi_of_ig_': FM> ../Modules/berry_phase.o(.text+0x61c2): undefined reference to `ln_ind_' FM> ../Modules/berry_phase.o(.text+0x6362): undefined reference to `ln_ind_' FM> ../Modules/berry_phase.o(.text+0x63e2): undefined reference to `ln_ind_' FM> ../Modules/berry_phase.o(.text+0x6452): undefined reference to `ln_ind_' FM> ../Modules/berry_phase.o(.text+0x6572): undefined reference to `ln_ind_' FM> ../Modules/berry_phase.o(.text+0x6602): more undefined references to FM> `ln_ind_' follow FM> make[1]: *** [pw.x] Error 1 FM> make[1]: Leaving directory `/home.snfs/fjma/pw3.2/espresso-3.2/PW' FM> make: *** [pw] Error 2 FM> FM> Yours, FM> Ma FM> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From giannozz at nest.sns.it Mon Dec 11 12:08:46 2006 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 11 Dec 2006 12:08:46 +0100 Subject: [Pw_forum] El-ph and spin not implemented In-Reply-To: References: Message-ID: On Dec 11, 2006, at 5:44 , Amit Kumar wrote: > I'm getting the following error for an AFM metal. > > El-ph and spin not implemented > > My questions is, in the new version of pwscf is it implemented???? no, but it shouldn't be that difficult to implement. > It would be better if you add a page in new user guide describing > what's new in the current version compare to the previous versions. it would. There is a file "ChangeLog" that details all changes, though > Why I'm not finding the executable LAMBDA.X in the executable > directory of PWSCF after compilation??? because lambda.f90 is not really ready for use; it is provided "as is", just as an example. The last version uses a different processing of the electron-phonon data that is undocumented for the same reason. Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From degironc at sissa.it Mon Dec 11 12:55:29 2006 From: degironc at sissa.it (degironc) Date: Mon, 11 Dec 2006 12:55:29 +0100 Subject: [Pw_forum] Magnetic moment on each atom In-Reply-To: <9d7293e10612061655l2dd72da8o17755d5118d24ae1@mail.gmail.com> References: <9d7293e10612061655l2dd72da8o17755d5118d24ae1@mail.gmail.com> Message-ID: <457D4731.1000405@sissa.it> As Axel was explaining there is no "right" way of defining the local magnetic moment around an atom in a multi-atom system. However an aproximate way to definie it is via the projected density of states on the atomic orbitals (code projwfc.x, see example08 for its use as a postprocessing tool). This code generate many files with the density of states projected on each atomic wavefunction of each atom and a BIG amount of data on the standard output, the last few lines of which contain the decomposition of Lowdin charges on angular momentum and spin component of each atom. In the example08 (bulk nickel, file ni.pdos.out) these lines looks like.. #-------------- Lowdin Charges: Atom # 1: total charge = 9.8849, s, p, d, f = 0.9348 0.0000 8.9501 spin up = 5.2271, s, p, d, f = 0.4610 0.0000 4.7661 spin down = 4.6578, s, p, d, f = 0.4738 0.0000 4.1840 polarization = 0.5693, s, p, d, f = -0.0128 0.0000 0.5821 Spilling Parameter: 0.0115 #--------------- This is probably close to the information you are looking for. stefano Jess Kondor wrote: > Hello, everyone > > I am studying the magnetic systems. The code (pwscf) prints > absolute and total magnetization. Is there a way to get the magnetic > moment of each atom in the unit cell? > > Thanks, > JK > > From nguyenhalvt at yahoo.com Mon Dec 11 14:28:32 2006 From: nguyenhalvt at yahoo.com (Nguyen Ngoc Ha) Date: Mon, 11 Dec 2006 05:28:32 -0800 (PST) Subject: [Pw_forum] Calculation of Fukui function? Message-ID: <298357.74955.qm@web31006.mail.mud.yahoo.com> Dear PWscf Users! I like to calculale Fukui function with PWscf, I don't know if PWscf can? Please help me to do that! Best Regards! Nguyen, Ngoc Ha Hanoi University of Education Faculty of Chemistry Department of Physical Chemistry Tel: Office: 04/8330842 Home: 04/7681083 Mobile: 0912129517 ____________________________________________________________________________________ Yahoo! Music Unlimited Access over 1 million songs. http://music.yahoo.com/unlimited From akohlmey at cmm.chem.upenn.edu Mon Dec 11 16:27:11 2006 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Mon, 11 Dec 2006 10:27:11 -0500 (EST) Subject: [Pw_forum] Calculation of Fukui function? In-Reply-To: <298357.74955.qm@web31006.mail.mud.yahoo.com> Message-ID: On Mon, 11 Dec 2006, Nguyen Ngoc Ha wrote: NH> Dear PWscf Users! NH> I like to calculale Fukui function with PWscf, NH> I don't know if PWscf can? Please help me to do that! if you don't know where to start looking: grep is your friend! go to the quantum espresso (source) directory and do, e.g.: grep -i fukui */* or grep -i fukui */*.f* in case you want to narrow down the search to the source code and speed up matters. both come up empty, i.e. it is unlikely that the code can compute what you want. cheers, axel. NH> Best Regards! NH> NH> Nguyen, Ngoc Ha NH> Hanoi University of Education NH> Faculty of Chemistry NH> Department of Physical Chemistry NH> Tel: Office: 04/8330842 NH> Home: 04/7681083 NH> Mobile: 0912129517 NH> NH> NH> NH> ____________________________________________________________________________________ NH> Yahoo! Music Unlimited NH> Access over 1 million songs. NH> http://music.yahoo.com/unlimited NH> _______________________________________________ NH> Pw_forum mailing list NH> Pw_forum at pwscf.org NH> http://www.democritos.it/mailman/listinfo/pw_forum NH> -- ======================================================================= 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 Dec 11 17:08:20 2006 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Mon, 11 Dec 2006 11:08:20 -0500 (EST) Subject: [Pw_forum] use doual core In-Reply-To: <004601c71cce$c1a8bbd0$1d00a8c0@solarflare> Message-ID: On Mon, 11 Dec 2006, Huiqun Zhou wrote: HZ> Amin, HZ> HZ> In addition to Axel's suggustions, you may need to add -D__MPI option too. true, but please note, that i suggested to look for -D__PARA as indicator that configure picked up the MPI library and recommended to re-run configure. that will make sure that _everything_ is set up properly (including preprocessing!). changing makefiles is ok, if you know what you are doing, but having configure do this for you is the safer way in 99% of the cases, especially for people with little experience in compiling research codes. ;-) cheers, axel. HZ> HZ> Huiqun HZ> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From giannozz at nest.sns.it Mon Dec 11 17:13:15 2006 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 11 Dec 2006 17:13:15 +0100 Subject: [Pw_forum] Calculation of Fukui function? In-Reply-To: References: Message-ID: <51EAE016-8143-47AC-85F7-7DDC709F9CEA@nest.sns.it> On Dec 11, 2006, at 16:27 , Axel Kohlmeyer wrote: > On Mon, 11 Dec 2006, Nguyen Ngoc Ha wrote: > > NH> Dear PWscf Users! > NH> I like to calculale Fukui function with PWscf, > NH> I don't know if PWscf can? Please help me to do that! > > if you don't know where to start looking: grep is your friend! and if you never heard about Fukui functions (I didn't): google is your friend... http://www.iupac.org/reports/1999/7110minkin/f.html#frontier_function > both come up empty, i.e. it is unlikely that > the code can compute what you want. one possibility is to compute a system with N and N+delta electrons and perform a finite-difference derivativation of the charge density. It can be done using pp.x . Not sure how well it works. Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From babazade at gmail.com Mon Dec 11 18:52:23 2006 From: babazade at gmail.com (Amin Babazadeh) Date: Mon, 11 Dec 2006 21:22:23 +0330 Subject: [Pw_forum] problem with k-points In-Reply-To: <20061210162015.13029.qmail@webmail58.rediffmail.com> References: <20061210162015.13029.qmail@webmail58.rediffmail.com> Message-ID: Hi Sanjeev For band calculation you should first find the symmetry point of you cell and then make a k point.because when you plot the band structure it means that you like to know about variation of energy in e spatial direction so this direction is arbitrary(the best direction is the direction of symmetry point).you can also use Xcrysdan for this job or use the examples k-point (esample01) about the Fermi energy emine said your answer.we use Fermi energy to set a beginning point for plotting dos or band structure. best the regards amin On 10 Dec 2006 16:20:15 -0000, Sanjeev Kumar Gupta < sanjeev0302 at rediffmail.com> wrote: > > Thanking you Amin, > > >>This is done in espresso code automatically for scf and nscf but for > plotting band structure you should do it manually>> > > But what will be the maximum and minimum range of the k-point for band > calculation and also you said in earlier suggestion that, for scf and nscf > it is automatic,but we want to do manually the how we will proceeds? > > >>I thought it is possible.negative or positive Fermi energy doesn't have > physical meaning>> > > sorry, for again same question, what is significance of negative fermi > energy is any relation in other calculation. > > I want to find out the elastic constant for my system, how we will > proceeds? > > > Regards > sanjeev > > > On Sun, 10 Dec 2006 Amin Babazadeh wrote : > >Dear sanjeev > > > > > > > >On 9 Dec 2006 04:44:31 -0000, Sanjeev Kumar Gupta < > >sanjeev0302 at rediffmail.com> wrote: > >> > >>Respected sir, > >> > >>i am sanjeev gupta, from india, working DFT calculation via > >>Quantum-Espresso-3.1.1. I have doubts with k-ponits, > >>1)How we choose k-points for diiferent system? > >> > > > >dis is done in espresso code automatically for scf and nscf but for > plotting > >band structure you should do it manually > > > >2)Is possible fermi energy negative for noble nitrides? > >> > >. > > > > > >3)Is neccessary same k-points for scf and nscf cycle or phX,phL and phG.? > >>no you can change it.for scf and nscf.usually the kpoint for scf > >>calculation is smaller than nscf.about phX,phL and phG i don't have any > >>idea. > >> > > > >good luck > >amin > > > >with regards > >>sanjeev gupta > >> > >>==================================================== > >>Sanjeev Kumar Gupta > >>Junior Research Fellow (DAE-BRNS) > >>Computational Condensed Matter Physics Lab.(CCMP) > >>Department of Physics, Faculty of Science, > >>The M.S.University of Baroda, Vadodara - 390 002. > >>Ph.No: +91-265-279 5339 (O) extn: 30-25 > >>mobile:09374616019 > >>Email: sanjeev0302 at rediffmail.com > >> sanjeev0302 at yahoo.co.in > >> skgupta-phy at msubaroda.ac.in > >>==================================================== > >> > >>Residential Address- > >> > >>Dr. Vikram Sarabhai Hall, > >>Room No.-95, Boys' Hostel,M.S.University Campus, > >>Pratapgunj,Vadodara-390 002,Gujarat,INDIA > >> > >> > >> > >>< > http://adworks.rediff.com/cgi-bin/AdWorks/sigclick.cgi/www.rediff.com/signature-home.htm/1507191490 at Middle5?PARTNER=3 > > > > > > > > > > > >-- AMIN > ==================================================== > Sanjeev Kumar Gupta > Junior Research Fellow (DAE-BRNS) > Computational Condensed Matter Physics Lab.(CCMP) > Department of Physics, Faculty of Science, > The M.S.University of Baroda, Vadodara - 390 002. > Ph.No: +91-265-279 5339 (O) extn: 30-25 > mobile:09374616019 > Email: sanjeev0302 at rediffmail.com > sanjeev0302 at yahoo.co.in > skgupta-phy at msubaroda.ac.in > ==================================================== > > Residential Address- > > Dr. Vikram Sarabhai Hall, > Room No.-95, Boys' Hostel,M.S.University Campus, > Pratapgunj,Vadodara-390 002,Gujarat,INDIA > > > > -- AMIN -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061211/18c226de/attachment.htm From babazade at gmail.com Mon Dec 11 19:06:39 2006 From: babazade at gmail.com (Amin Babazadeh) Date: Mon, 11 Dec 2006 21:36:39 +0330 Subject: [Pw_forum] use doual core In-Reply-To: References: <004601c71cce$c1a8bbd0$1d00a8c0@solarflare> Message-ID: Dear Axel I did the the env MPIF90=mpif77 ./configure command and it works very good and also i check the -D__PARA and more than it i saw that at the end of configuration it had been write the parallel computation detect. I think that all of the thing is OK. I am so appreciate your help. best the wishes amin On 12/11/06, Axel Kohlmeyer wrote: > > On Mon, 11 Dec 2006, Huiqun Zhou wrote: > > HZ> Amin, > HZ> > HZ> In addition to Axel's suggustions, you may need to add -D__MPI option > too. > > true, but please note, that i suggested to look for -D__PARA as > indicator that configure picked up the MPI library and recommended > to re-run configure. that will make sure that _everything_ is set up > properly (including preprocessing!). changing makefiles is ok, if > you know what you are doing, but having configure do this for you > is the safer way in 99% of the cases, especially for people with > little experience in compiling research codes. ;-) > > cheers, > axel. > > HZ> > HZ> Huiqun > HZ> > -- > ======================================================================= > 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 > -- AMIN -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061211/5a0f7fa4/attachment.htm From amit76.india at gmail.com Tue Dec 12 07:22:04 2006 From: amit76.india at gmail.com (Amit Kumar) Date: Tue, 12 Dec 2006 11:52:04 +0530 Subject: [Pw_forum] El-ph coupling Lambda Message-ID: Dear Users, I think there is a mismatch in README and RUN_EXAMPLE files of Example 7. I see the following line in the README file. Calculate lambda coefficient (in file "lambda") and the a^2F(omega) function using "matdyn.x" (dos=.true.) But no lambda file in run_example of that example. Could anyone send me the input file for calculating Lambda coefficient or any useful reference to know more about El-ph coupling??? I'm very much interested to know more about the post processing methods after getting the output of ph.x. I'll be highly obliged if someone help me to learn the El-ph coupling calculation using pwscf. Dear Prof. Paolo, would you like to give me some hints how to implement El-ph coupling and spin together??? Looking forward to your suggestions. Regards, Amit -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061212/24fe6041/attachment.htm From baroni at sissa.it Tue Dec 12 08:12:22 2006 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 12 Dec 2006 08:12:22 +0100 Subject: [Pw_forum] El-ph coupling Lambda In-Reply-To: References: Message-ID: Dear Amit: On Dec 12, 2006, at 7:22 AM, Amit Kumar wrote: > Dear Prof. Paolo, would you like to give me some hints how to > implement > El-ph coupling and spin together??? It is very difficult for to give you "some hints" without knowing what are your needs and, above all, what is your background. "Hints" may go anywhere in between reading a chapter of a textbook in solid- state physics (or even elementary quantum mechanics), to very sophisticated and esoteric physics or implementation issues. Please: state your problem ("where I want to go") and your background ("where will I start from"), and we we'll make our best to help you. Be advised, though, that if your problem is not focused enough (e.g. "I want to write a PhD thesis on el-ph interactions" would definitely not qualify as a well defined problem) or if your background is too remote from your present aim, people in a technical form such as this one can hardly be of any practical help. > Looking forward to your suggestions. looking forward to *your* further hints Stefano --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061212/24b83478/attachment.htm From baroni at sissa.it Tue Dec 12 08:21:48 2006 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 12 Dec 2006 08:21:48 +0100 Subject: [Pw_forum] Calculation of Fukui function? In-Reply-To: <51EAE016-8143-47AC-85F7-7DDC709F9CEA@nest.sns.it> References: <51EAE016-8143-47AC-85F7-7DDC709F9CEA@nest.sns.it> Message-ID: On Dec 11, 2006, at 5:13 PM, Paolo Giannozzi wrote: > > On Dec 11, 2006, at 16:27 , Axel Kohlmeyer wrote: > >> On Mon, 11 Dec 2006, Nguyen Ngoc Ha wrote: >> >> NH> Dear PWscf Users! >> NH> I like to calculale Fukui function with PWscf, >> NH> I don't know if PWscf can? Please help me to do that! >> >> if you don't know where to start looking: grep is your friend! > > and if you never heard about Fukui functions (I didn't): > google is your friend... > http://www.iupac.org/reports/1999/7110minkin/f.html#frontier_function I may have totally misunderstood the obscure definition of the "Fukui function" (which, by the way I too never heard about before) given above, but it seems to me that it is simply (or it is simply related to) the local density of states at the Fermi energy. If this is the case, doesn't any tool in pp.x or elsewhere already calculate that? Stefano --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061212/74ebb9ff/attachment.htm From degironc at sissa.it Tue Dec 12 09:00:03 2006 From: degironc at sissa.it (degironc) Date: Tue, 12 Dec 2006 09:00:03 +0100 Subject: [Pw_forum] Calculation of Fukui function? In-Reply-To: References: <51EAE016-8143-47AC-85F7-7DDC709F9CEA@nest.sns.it> Message-ID: <457E6183.9020401@sissa.it> Stefano Baroni wrote: > On Dec 11, 2006, at 5:13 PM, Paolo Giannozzi wrote: > >> >> On Dec 11, 2006, at 16:27 , Axel Kohlmeyer wrote: >> >>> On Mon, 11 Dec 2006, Nguyen Ngoc Ha wrote: >>> >>> NH> Dear PWscf Users! >>> NH> I like to calculale Fukui function with PWscf, >>> NH> I don't know if PWscf can? Please help me to do that! >>> >>> if you don't know where to start looking: grep is your friend! >> >> >> and if you never heard about Fukui functions (I didn't): >> google is your friend... >> http://www.iupac.org/reports/1999/7110minkin/f.html#frontier_function > > > I may have totally misunderstood the obscure definition of the "Fukui > function" (which, by the way I too never heard about before) given > above, but it seems to me that it is simply (or it is simply related > to) the local density of states at the Fermi energy. If this is the > case, doesn't any tool in pp.x or elsewhere already calculate that? yes, the post-processing tool pp.x with plot_num=3 is just that. more information in Doc/INPUT_PP stefano > Stefano > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste > [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > From yuwen_66 at yahoo.com Tue Dec 12 10:07:34 2006 From: yuwen_66 at yahoo.com (W. YU) Date: Tue, 12 Dec 2006 01:07:34 -0800 (PST) Subject: [Pw_forum] cannot bracket Ef error Message-ID: <192323.61726.qm@web51014.mail.yahoo.com> Dear PW users, I have been doing a calculation on an antiferromagnetic system. The SCF job goes well. But I kept getting the following error message when I tried to do a band structure job: ======================= from efermig: error # 1 internal error, cannot bracket Ef. =================================== Note: I also got the "one eigenvalue not converged" warning many times before the final error for fermi energy locating if I use david diagonalization but conjugate gradient method suppress it. ==================================================== I have browsed this forum and found little information about this. I tried to change kpoint grid and mixing schem but it doesn't work. Prof. Paolo said there are some alternatives to the smearing technique. Do you mean "tetrahedra" or something elese. I think "tetrahedra" works only for dos calculation. Could anybody help me with this problem? The following is a link to my input file: http://www.geocities.com/yuwen_66/run_li2cuo2_band.htm Best regards, Wen YU ____________________________________________________________________________________ Do you Yahoo!? Everyone is raving about the all-new Yahoo! Mail beta. http://new.mail.yahoo.com From sanjeev0302 at rediffmail.com Tue Dec 12 10:31:50 2006 From: sanjeev0302 at rediffmail.com (Sanjeev Kumar Gupta) Date: 12 Dec 2006 09:31:50 -0000 Subject: [Pw_forum] problem with k-points Message-ID: <20061212093150.24225.qmail@webmail53.rediffmail.com> ? Thanking You Amin, I am step_4 , want to calculate elastic constant and electronic DOS? At this step, is any specific k-points or same as we have taken in scf and nscf. one another confusion, is that , it is neccessary k-points same in scf,nscf,bands,phX, phG,phL? how we will choose k-points for these diiferent calculation? s.k.gupta On Mon, 11 Dec 2006 Amin Babazadeh wrote : >Hi Sanjeev >For band calculation you should first find the symmetry point of you cell >and then make a k point.because when you plot the band structure it means >that you like to know about variation of energy in e spatial direction so >this direction is arbitrary(the best direction is the direction of symmetry >point).you can also use Xcrysdan for this job or use the examples k-point >(esample01) >about the Fermi energy emine said your answer.we use Fermi energy to set a >beginning point for plotting dos or band structure. >best the regards >amin > >On 10 Dec 2006 16:20:15 -0000, Sanjeev Kumar Gupta < >sanjeev0302 at rediffmail.com> wrote: >> >>Thanking you Amin, >> >> >>This is done in espresso code automatically for scf and nscf but for >>plotting band structure you should do it manually>> >> >>But what will be the maximum and minimum range of the k-point for band >>calculation and also you said in earlier suggestion that, for scf and nscf >>it is automatic,but we want to do manually the how we will proceeds? >> >> >>I thought it is possible.negative or positive Fermi energy doesn't have >>physical meaning>> >> >>sorry, for again same question, what is significance of negative fermi >>energy is any relation in other calculation. >> >>I want to find out the elastic constant for my system, how we will >>proceeds? >> >> >>Regards >>sanjeev >> >> >>On Sun, 10 Dec 2006 Amin Babazadeh wrote : >> >Dear sanjeev >> > >> > >> > >> >On 9 Dec 2006 04:44:31 -0000, Sanjeev Kumar Gupta < >> >sanjeev0302 at rediffmail.com> wrote: >> >> >> >>Respected sir, >> >> >> >>i am sanjeev gupta, from india, working DFT calculation via >> >>Quantum-Espresso-3.1.1. I have doubts with k-ponits, >> >>1)How we choose k-points for diiferent system? >> >> >> > >> >dis is done in espresso code automatically for scf and nscf but for >>plotting >> >band structure you should do it manually >> > >> >2)Is possible fermi energy negative for noble nitrides? >> >> >> >. >> > >> > >> >3)Is neccessary same k-points for scf and nscf cycle or phX,phL and phG.? >> >>no you can change it.for scf and nscf.usually the kpoint for scf >> >>calculation is smaller than nscf.about phX,phL and phG i don't have any >> >>idea. >> >> >> > >> >good luck >> >amin >> > >> >with regards >> >>sanjeev gupta >> >> >> >>==================================================== >> >>Sanjeev Kumar Gupta >> >>Junior Research Fellow (DAE-BRNS) >> >>Computational Condensed Matter Physics Lab.(CCMP) >> >>Department of Physics, Faculty of Science, >> >>The M.S.University of Baroda, Vadodara - 390 002. >> >>Ph.No: +91-265-279 5339 (O) extn: 30-25 >> >>mobile:09374616019 >> >>Email: sanjeev0302 at rediffmail.com >> >> sanjeev0302 at yahoo.co.in >> >> skgupta-phy at msubaroda.ac.in >> >>==================================================== >> >> >> >>Residential Address- >> >> >> >>Dr. Vikram Sarabhai Hall, >> >>Room No.-95, Boys' Hostel,M.S.University Campus, >> >>Pratapgunj,Vadodara-390 002,Gujarat,INDIA >> >> >> >> >> >> >> >>< >>http://adworks.rediff.com/cgi-bin/AdWorks/sigclick.cgi/www.rediff.com/signature-home.htm/1507191490 at Middle5?PARTNER=3 >> > >> > >> > >> > >> > >> >-- AMIN >>==================================================== >>Sanjeev Kumar Gupta >>Junior Research Fellow (DAE-BRNS) >>Computational Condensed Matter Physics Lab.(CCMP) >>Department of Physics, Faculty of Science, >>The M.S.University of Baroda, Vadodara - 390 002. >>Ph.No: +91-265-279 5339 (O) extn: 30-25 >>mobile:09374616019 >>Email: sanjeev0302 at rediffmail.com >> sanjeev0302 at yahoo.co.in >> skgupta-phy at msubaroda.ac.in >>==================================================== >> >>Residential Address- >> >>Dr. Vikram Sarabhai Hall, >>Room No.-95, Boys' Hostel,M.S.University Campus, >>Pratapgunj,Vadodara-390 002,Gujarat,INDIA >> >> >> >> > > > > >-- AMIN ==================================================== Sanjeev Kumar Gupta Junior Research Fellow (DAE-BRNS) Computational Condensed Matter Physics Lab.(CCMP) Department of Physics, Faculty of Science, The M.S.University of Baroda, Vadodara - 390 002. Ph.No: +91-265-279 5339 (O) extn: 30-25 mobile:09374616019 Email: sanjeev0302 at rediffmail.com sanjeev0302 at yahoo.co.in skgupta-phy at msubaroda.ac.in ==================================================== Residential Address- Dr. Vikram Sarabhai Hall, Room No.-95, Boys' Hostel,M.S.University Campus, Pratapgunj,Vadodara-390 002,Gujarat,INDIA -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061212/b43ea4d5/attachment.htm From babazade at gmail.com Tue Dec 12 13:09:41 2006 From: babazade at gmail.com (Amin Babazadeh) Date: Tue, 12 Dec 2006 15:39:41 +0330 Subject: [Pw_forum] problem with k-points In-Reply-To: <20061212093150.24225.qmail@webmail53.rediffmail.com> References: <20061212093150.24225.qmail@webmail53.rediffmail.com> Message-ID: Dear Sanjeev I haven't done the elastic constant until yet so i don't have any idea about it. i think the best way is looking to the examples. in the example you can see where you should select automatic k point or manual. best the wishes amin On 12 Dec 2006 09:31:50 -0000, Sanjeev Kumar Gupta < sanjeev0302 at rediffmail.com> wrote: > > > Thanking You Amin, > > I am step_4 , want to calculate elastic constant and electronic DOS? > At this step, is any specific k-points or same as we have taken in scf and > nscf. > > > one another confusion, is that , it is neccessary k-points same in > scf,nscf,bands,phX, phG,phL? how we will choose k-points for these diiferent > calculation? > > s.k.gupta > > > On Mon, 11 Dec 2006 Amin Babazadeh wrote : > >Hi Sanjeev > >For band calculation you should first find the symmetry point of you cell > >and then make a k point.because when you plot the band structure it means > >that you like to know about variation of energy in e spatial direction so > >this direction is arbitrary(the best direction is the direction of > symmetry > >point).you can also use Xcrysdan for this job or use the examples k-point > >(esample01) > >about the Fermi energy emine said your answer.we use Fermi energy to set > a > >beginning point for plotting dos or band structure. > >best the regards > >amin > > > >On 10 Dec 2006 16:20:15 -0000, Sanjeev Kumar Gupta < > >sanjeev0302 at rediffmail.com> wrote: > >> > >>Thanking you Amin, > >> > >> >>This is done in espresso code automatically for scf and nscf but for > >>plotting band structure you should do it manually>> > >> > >>But what will be the maximum and minimum range of the k-point for band > >>calculation and also you said in earlier suggestion that, for scf and > nscf > >>it is automatic,but we want to do manually the how we will proceeds? > >> > >> >>I thought it is possible.negative or positive Fermi energy doesn't > have > >>physical meaning>> > >> > >>sorry, for again same question, what is significance of negative fermi > >>energy is any relation in other calculation. > >> > >>I want to find out the elastic constant for my system, how we will > >>proceeds? > >> > >> > >>Regards > >>sanjeev > >> > >> > >>On Sun, 10 Dec 2006 Amin Babazadeh wrote : > >> >Dear sanjeev > >> > > >> > > >> > > >> >On 9 Dec 2006 04:44:31 -0000, Sanjeev Kumar Gupta < > >> >sanjeev0302 at rediffmail.com> wrote: > >> >> > >> >>Respected sir, > >> >> > >> >>i am sanjeev gupta, from india, working DFT calculation via > >> >>Quantum-Espresso-3.1.1. I have doubts with k-ponits, > >> >>1)How we choose k-points for diiferent system? > >> >> > >> > > >> >dis is done in espresso code automatically for scf and nscf but for > >>plotting > >> >band structure you should do it manually > >> > > >> >2)Is possible fermi energy negative for noble nitrides? > >> >> > >> >. > >> > > >> > > >> >3)Is neccessary same k-points for scf and nscf cycle or phX,phL and > phG.? > >> >>no you can change it.for scf and nscf.usually the kpoint for scf > >> >>calculation is smaller than nscf.about phX,phL and phG i don't have > any > >> >>idea. > >> >> > >> > > >> >good luck > >> >amin > >> > > >> >with regards > >> >>sanjeev gupta > >> >> > >> >>==================================================== > >> >>Sanjeev Kumar Gupta > >> >>Junior Research Fellow (DAE-BRNS) > >> >>Computational Condensed Matter Physics Lab.(CCMP) > >> >>Department of Physics, Faculty of Science, > >> >>The M.S.University of Baroda, Vadodara - 390 002. > >> >>Ph.No: +91-265-279 5339 (O) extn: 30-25 > >> >>mobile:09374616019 > >> >>Email: sanjeev0302 at rediffmail.com > >> >> sanjeev0302 at yahoo.co.in > >> >> skgupta-phy at msubaroda.ac.in > >> >>==================================================== > >> >> > >> >>Residential Address- > >> >> > >> >>Dr. Vikram Sarabhai Hall, > >> >>Room No.-95, Boys' Hostel,M.S.University Campus, > >> >>Pratapgunj,Vadodara-390 002,Gujarat,INDIA > >> >> > >> >> > >> >> > >> >>< > >>http://adworks.rediff.com/cgi-bin/AdWorks/sigclick.cgi/www.rediff.com/signature-home.htm/1507191490 at Middle5?PARTNER=3 > > >> > > >> > > >> > > >> > > >> > > >> >-- AMIN > >>==================================================== > >>Sanjeev Kumar Gupta > >>Junior Research Fellow (DAE-BRNS) > >>Computational Condensed Matter Physics Lab.(CCMP) > >>Department of Physics, Faculty of Science, > >>The M.S.University of Baroda, Vadodara - 390 002. > >>Ph.No: +91-265-279 5339 (O) extn: 30-25 > >>mobile:09374616019 > >>Email: sanjeev0302 at rediffmail.com > >> sanjeev0302 at yahoo.co.in > >> skgupta-phy at msubaroda.ac.in > >>==================================================== > >> > >>Residential Address- > >> > >>Dr. Vikram Sarabhai Hall, > >>Room No.-95, Boys' Hostel,M.S.University Campus, > >>Pratapgunj,Vadodara-390 002,Gujarat,INDIA > >> > >> > >> > >> > > > > > > > > > > >-- AMIN > ==================================================== > Sanjeev Kumar Gupta > Junior Research Fellow (DAE-BRNS) > Computational Condensed Matter Physics Lab.(CCMP) > Department of Physics, Faculty of Science, > The M.S.University of Baroda, Vadodara - 390 002. > Ph.No: +91-265-279 5339 (O) extn: 30-25 > mobile:09374616019 > Email: sanjeev0302 at rediffmail.com > sanjeev0302 at yahoo.co.in > skgupta-phy at msubaroda.ac.in > ==================================================== > > Residential Address- > > Dr. Vikram Sarabhai Hall, > Room No.-95, Boys' Hostel,M.S.University Campus, > Pratapgunj,Vadodara-390 002,Gujarat,INDIA > > > -- AMIN -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061212/c3c7c8a5/attachment.htm From babazade at gmail.com Tue Dec 12 13:37:37 2006 From: babazade at gmail.com (Amin Babazadeh) Date: Tue, 12 Dec 2006 16:07:37 +0330 Subject: [Pw_forum] permittivity Message-ID: dear users I work with quantum espresso code and i want to know if we can find optical properties (permittivity, susceptibility, absorption,....) with using this cod. i search in the examples but i couldn't;t find any thing. i will appreciate your help -- AMIN -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061212/f2cbbc33/attachment.htm From degironc at sissa.it Tue Dec 12 14:16:25 2006 From: degironc at sissa.it (degironc) Date: Tue, 12 Dec 2006 14:16:25 +0100 Subject: [Pw_forum] cannot bracket Ef error In-Reply-To: <192323.61726.qm@web51014.mail.yahoo.com> References: <192323.61726.qm@web51014.mail.yahoo.com> Message-ID: <457EABA9.1060208@sissa.it> W. YU wrote: >Dear PW users, > >I have been doing a calculation on an >antiferromagnetic system. The SCF job goes well. But I >kept getting the following error message when I tried >to do a band structure job: > > you should not specify calculation='nscf' but calculation='bands' for band structure run. stefano >======================= >from efermig: error # 1 >internal error, cannot bracket Ef. >=================================== >Note: I also got the "one eigenvalue not converged" >warning many times before the final error for fermi >energy locating if I use david diagonalization but >conjugate gradient method suppress it. >==================================================== >I have browsed this forum and found little information >about this. I tried to change kpoint grid and mixing >schem but it doesn't work. Prof. Paolo said there are >some alternatives to the smearing technique. Do you >mean "tetrahedra" or something elese. I think >"tetrahedra" works only for dos calculation. > >Could anybody help me with this problem? > >The following is a link to my input file: > >http://www.geocities.com/yuwen_66/run_li2cuo2_band.htm > >Best regards, > >Wen YU > > > > > >____________________________________________________________________________________ >Do you Yahoo!? >Everyone is raving about the all-new Yahoo! Mail beta. >http://new.mail.yahoo.com >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > From srijan.india at gmail.com Tue Dec 12 15:05:49 2006 From: srijan.india at gmail.com (Srijan Kumar Saha) Date: Tue, 12 Dec 2006 19:35:49 +0530 Subject: [Pw_forum] compilation error Message-ID: <3fcc7e670612120605r36efeb98pe0309b084cfa6957@mail.gmail.com> Dear pwscf Users, I have configured the new version of PWSCF on my computer. But I'm getting the following error during compilation. >>>>>>make all test -d bin || mkdir bin if test -d iotk ; then \ ( cd iotk ; if test "make" = "" ; then make TLDEPS= libiotk.a ; \ else make TLDEPS= libiotk.a ; fi ) ; fi make[1]: Entering directory `/home2/srijan/e3.2/iotk' cd src ; make libiotk.a make[2]: Entering directory `/home2/srijan/e3.2/iotk/src' make[2]: `libiotk.a' is up to date. make[2]: Leaving directory `/home2/srijan/e3.2/iotk/src' make[1]: Leaving directory `/home2/srijan/e3.2/iotk' ( cd Modules ; if test "make" = "" ; then make TLDEPS= all ; \ else make TLDEPS= all ; fi ) make[1]: Entering directory `/home2/srijan/e3.2/Modules' ifort -O2 -tpp6 -assume byterecl -nomodule -fpp -D__INTEL -D__FFTW -D__USE_INTERNAL_FFTW -I../include -I./ -I../Modules -I../iotk/src -I../PW -I../PH -I../CPV -c constraints_module.f90 0_6374 fortcom: Severe: **Internal compiler error: internal abort** Please report this error along with the circumstances in which it occurred in a Software Problem Report. Note: File and line given may not be explicit cause of this error. in file (null), line 0, column 0 compilation aborted for constraints_module.f90 (code 3) make[1]: *** [constraints_module.o] Error 3 make[1]: Leaving directory `/home2/srijan/e3.2/Modules' make: *** [mods] Error 2 What should I do to get rid of this error? With best regards, Srijan -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061212/31452a3d/attachment.htm From amit76.india at gmail.com Tue Dec 12 15:24:25 2006 From: amit76.india at gmail.com (Amit Kumar) Date: Tue, 12 Dec 2006 19:54:25 +0530 Subject: [Pw_forum] El-ph coupling Message-ID: Respected Sir, >>>>>>>>> Dear Prof. Paolo, would you like to give me some hints how to implement El-ph coupling and spin together??? I asked the above question on reply of Prof. Paolo's last letter to me. So I think my question is not so defocussed. Well, let me put my question more specifically. Example No.7 calculates the elctron phonon coupling of Al (with nspin=1) What I have to modify to calculate the same thing for a magnetic metal (suppose Ni)???? If I change nspin=2 then pwscf is saying that El-ph coupling and spin not implemented yet. So I need some suggestions to handle this problem. Regards, Amit -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061212/d193a9fd/attachment.htm From baroni at sissa.it Tue Dec 12 15:25:27 2006 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 12 Dec 2006 15:25:27 +0100 Subject: [Pw_forum] compilation error In-Reply-To: <3fcc7e670612120605r36efeb98pe0309b084cfa6957@mail.gmail.com> References: <3fcc7e670612120605r36efeb98pe0309b084cfa6957@mail.gmail.com> Message-ID: <80FA4FEA-0022-48DE-9CBE-7BAB5F53E34C@sissa.it> Dear Srijan, let me save the time of the many people that have already answered many times similar questions in the past. On Dec 12, 2006, at 3:05 PM, Srijan Kumar Saha wrote: > make[1]: Entering directory `/home2/srijan/e3.2/Modules' > ifort -O2 -tpp6 -assume byterecl -nomodule -fpp -D__INTEL -D__FFTW - > D__USE_INTERNAL_FFTW -I../include -I./ -I../Modules -I../iotk/ > src -I../PW -I../PH -I../CPV -c constraints_module.f90 > 0_6374 > > fortcom: Severe: **Internal compiler error: internal abort** Please > report this error along with the circumstances in which it occurred > in a Software Problem Report. Note: File and line given may not be > explicit cause of this error. > in file (null), line 0, column 0 > > compilation aborted for constraints_module.f90 (code 3) > make[1]: *** [constraints_module.o] Error 3 > make[1]: Leaving directory `/home2/srijan/e3.2/Modules' > make: *** [mods] Error 2 This is a bug of the compiler, NOT of the code. A compiler is supposed to compile an even wrong code, or else to report that the code contains some errors. If it doesn't, it is the compiler that does not work. Please, note that the "Software Problem Report" is a service of the company (intel in this case) that distributes the compiler. So, the first action to undertake is to report to them. > What should I do to get rid of this error? 1) Browse the archive of this mailing list where this kind of problems has been discussed several times. 2) Change the compiler and/or implement a workaround (if any have been suggested that would fit your particolar case) accordingly. Cheers - Stefano > > With best regards, > Srijan > --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061212/988e23fe/attachment.htm From akohlmey at cmm.chem.upenn.edu Tue Dec 12 16:27:55 2006 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 12 Dec 2006 10:27:55 -0500 Subject: [Pw_forum] El-ph coupling In-Reply-To: References: Message-ID: <7b6913e90612120727m306a473l6d5b20ba50f217c4@mail.gmail.com> On 12/12/06, Amit Kumar wrote: > > Respected Sir, > > > > >>>>>>>>> Dear Prof. Paolo, would you like to give me some hints how to > implement > > El-ph coupling and spin together??? dear amit, the first and foremost recommendation for people to implement something into QE and any other package is to _read_ the sourcecode to get acquainted with it. i.e. figure out the flow of control for simple (and not so simple) jobs that already work. that usually takes a while (and i don't mean a couple of hours ;-) ). if you feel ready to program something, you should check out the development cvs and perhaps first try to implement some trivial enhancement, so you can practice how to communicate your changes to the developers and learn how to work off a moving target (i.e. a living cvs archive). cheers, axel. > I asked the above question on reply of Prof. Paolo's last letter to me. > So I think my question is not so defocussed. > Well, let me put my question more specifically. > > Example No.7 calculates the elctron phonon coupling of Al (with nspin=1) > What I have to modify to calculate the same thing for a magnetic metal > (suppose Ni)???? > If I change nspin=2 then pwscf is saying that El-ph coupling and spin > not implemented yet. > So I need some suggestions to handle this problem. > > Regards, > Amit > > > -- ======================================================================= 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 babazade at gmail.com Tue Dec 12 17:32:07 2006 From: babazade at gmail.com (Amin Babazadeh) Date: Tue, 12 Dec 2006 20:02:07 +0330 Subject: [Pw_forum] compilation error In-Reply-To: <3fcc7e670612120605r36efeb98pe0309b084cfa6957@mail.gmail.com> References: <3fcc7e670612120605r36efeb98pe0309b084cfa6957@mail.gmail.com> Message-ID: Dear Srijan I thought your problem is in compiling ifort. I hope if you done these command step by step you will be finally compile the espresso. 1-get the trial ifort from intel web site and copy it in /etc. 2-install the ifort (according to what install file says) 3-do this command cp /etc/.../iforvars.sh /etc/profile.d 4-go to the espresso file and ./configure 5-be sure that in the make.sys file all of the F77=ifort (it means you want to compile espresso by ifort) 6-make all i hope you will get the succeed amin On 12/12/06, Srijan Kumar Saha wrote: > > > Dear pwscf Users, > > I have configured the new version of PWSCF on my computer. > But I'm getting the following error during compilation. > > > >>>>>>make all > > test -d bin || mkdir bin > if test -d iotk ; then \ > ( cd iotk ; if test "make" = "" ; then make TLDEPS= libiotk.a ; \ > else make TLDEPS= libiotk.a ; fi ) ; fi > make[1]: Entering directory `/home2/srijan/e3.2/iotk' > cd src ; make libiotk.a > make[2]: Entering directory `/home2/srijan/e3.2/iotk/src' > make[2]: `libiotk.a' is up to date. > make[2]: Leaving directory `/home2/srijan/e3.2/iotk/src' > make[1]: Leaving directory `/home2/srijan/e3.2/iotk' > ( cd Modules ; if test "make" = "" ; then make TLDEPS= all ; \ > else make TLDEPS= all ; fi ) > make[1]: Entering directory `/home2/srijan/e3.2/Modules' > ifort -O2 -tpp6 -assume byterecl -nomodule -fpp -D__INTEL -D__FFTW > -D__USE_INTERNAL_FFTW -I../include -I./ -I../Modules -I../iotk/src > -I../PW -I../PH -I../CPV -c constraints_module.f90 > 0_6374 > > fortcom: Severe: **Internal compiler error: internal abort** Please report > this error along with the circumstances in which it occurred in a Software > Problem Report. Note: File and line given may not be explicit cause of this > error. > in file (null), line 0, column 0 > > compilation aborted for constraints_module.f90 (code 3) > make[1]: *** [constraints_module.o] Error 3 > make[1]: Leaving directory `/home2/srijan/e3.2/Modules' > make: *** [mods] Error 2 > > > What should I do to get rid of this error? > > With best regards, > Srijan > > -- AMIN -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061212/db4e9b3d/attachment.htm From ferretti.andrea at unimore.it Tue Dec 12 17:35:26 2006 From: ferretti.andrea at unimore.it (Andrea Ferretti) Date: Tue, 12 Dec 2006 17:35:26 +0100 (CET) Subject: [Pw_forum] permittivity In-Reply-To: References: Message-ID: On Tue, 12 Dec 2006, Amin Babazadeh wrote: > dear users > I work with quantum espresso code and i want to know if we can find optical > properties (permittivity, susceptibility, absorption,....) with using this > cod. > i search in the examples but i couldn't;t find any thing. > i will appreciate your help > in the last release of espresso (v3.2) you can find the program PP/epsilon.f90: this is a simple code for the computation of optical properties (basically absorption) at the RPA level on the kohn-sham electronic structure, without the inclusion of local fields. The methods implemented and the input file are more or less described in Doc/eps_man.tex andrea From jess.kondor at gmail.com Tue Dec 12 18:21:23 2006 From: jess.kondor at gmail.com (Jess Kondor) Date: Tue, 12 Dec 2006 11:21:23 -0600 Subject: [Pw_forum] different lattice representation Message-ID: <9d7293e10612120921k3bb99e88jd925588c0905f53e@mail.gmail.com> Hello, everyone I have a question regarding how to set up lattice in pwscf. Usually I like present lattice in the following format ( aka vasp format) lattice: a0 (in angstrom) a11 a12 a13 a21 a22 a23 a31 a32 a33 and atomic coordinates in the fractional (crystal) format. So, I guessed that in pwscf it should be something like that: ibrav = 0 celldm(1) = 1.88973 (corresponds 1 Ang) CELL_PARAMETERS cubic a11 a12 a13 a21 a22 a23 a31 a32 a33 ATOMIC_POSITIONS {crystal} ..... Using this representation for my system (slab) I didn't get convergence at all, and after a long careful examination, I found that this is due to wrong geometry representation. To confirm this fact, I took the simple system from example25 in espresso distribution and changed lattice like: from ibrav= 0, celldm(1)=8.19 CELL_PARAMETERS 0.50 0.50 1.00 0.50 1.00 0.50 1.00 0.50 0.50 ATOMIC_POSITIONS {crystal} to ibrav= 0, celldm(1)=1.00 , CELL_PARAMETERS 4.95 4.95 8.19 4.95 8.19 4.95 8.19 4.95 4.95 I thought these are equivalent representation, but the code give me different cell volumes and I obtained the different total energy, completely different magnetic moments and long convergence in the second case. So, I suggest that this representation (case 2) is not correct. Am I right? Best regards, JK -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061212/2a9cc612/attachment.htm From giannozz at nest.sns.it Tue Dec 12 18:26:28 2006 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 12 Dec 2006 18:26:28 +0100 Subject: [Pw_forum] different lattice representation In-Reply-To: <9d7293e10612120921k3bb99e88jd925588c0905f53e@mail.gmail.com> References: <9d7293e10612120921k3bb99e88jd925588c0905f53e@mail.gmail.com> Message-ID: <32EDF954-F4CF-4AAF-8DD2-4F1B66E677A9@nest.sns.it> On Dec 12, 2006, at 18:21 , Jess Kondor wrote: > > from > ibrav= 0, celldm(1)=8.19 > CELL_PARAMETERS > 0.50 0.50 1.00 > 0.50 1.00 0.50 > 1.00 0.50 0.50 > ATOMIC_POSITIONS {crystal} > > to > ibrav= 0, celldm(1)=1.00 , > CELL_PARAMETERS > 4.95 4.95 8.19 > 4.95 8.19 4.95 > 8.19 4.95 4.95 8.19 * 0.5 = ? --- Paolo Giannozzi, Democritos and University of Udine, Italy From babazade at gmail.com Tue Dec 12 20:13:05 2006 From: babazade at gmail.com (Amin Babazadeh) Date: Tue, 12 Dec 2006 22:43:05 +0330 Subject: [Pw_forum] permittivity In-Reply-To: References: Message-ID: Dear Andrea Thanks a lot for your help. sincerely yours amin On 12/12/06, Andrea Ferretti wrote: > > > > On Tue, 12 Dec 2006, Amin Babazadeh wrote: > > > dear users > > I work with quantum espresso code and i want to know if we can find > optical > > properties (permittivity, susceptibility, absorption,....) with using > this > > cod. > > i search in the examples but i couldn't;t find any thing. > > i will appreciate your help > > > > in the last release of espresso (v3.2) you can find the program > PP/epsilon.f90: > this is a simple code for the computation of optical properties > (basically absorption) at the RPA > level on the kohn-sham electronic structure, without the inclusion of > local fields. The methods implemented and the input file are more or less > described in Doc/eps_man.tex > > andrea > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- AMIN -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061212/000fc110/attachment.htm From fengjie.ma at gmail.com Wed Dec 13 04:00:02 2006 From: fengjie.ma at gmail.com (Fengjie Ma) Date: Wed, 13 Dec 2006 11:00:02 +0800 Subject: [Pw_forum] problems using pp.x Message-ID: Hi all, When I used pp.x to analyse and plot data after "scf" and "nscf", I met some problems: 1. The INPUT is: ------------------------------------------------------------------------------ &inputpp prefix = 'ttt_relax', outdir = '/home.snfs/fjma/tmp_test/tmp_test/', filplot = 'test', plot_num = 3 & &plot nfile = 1 , filepp(1) = 'test' , weight(1) = 1.0 , iflag = 2 , output_format = 2, fileout = 'test.rho.dat', x0(1) =0.0, x0(2)=0.0, x0(3)=0.0, e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0, e2(1) =0.0, e2(2)=1.0, e2(3) = 0.0, nx=20, ny=20 & -------------------------------------------------------------------------------- and the error is : -------------------------------------------------------------------------------- nbndx = 40 nbnd = 40 natomwfc = 66 npwx = 23472 nelec = 66.00 nkb = 132 ngl = 13548 Calling punch_plot, plot_num = 3 IOS = ** %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from davcio : error # 10 i/o error in davcio %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... -------------------------------------------------------------------------------- 2. The INPUT is: ------------------------------------------------------------------------------ &inputpp prefix = 'ttt_relax', outdir = '/home.snfs/fjma/tmp_test/tmp_test/', filplot = 'test', plot_num = 7, kpoint= 26, kband= 33, & &plot nfile = 1 , filepp(1) = 'test' , weight(1) = 1.0 , iflag = 2 , output_format = 2, fileout = 'test.rho.dat', x0(1) =0.0, x0(2)=0.0, x0(3)=0.0, e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0, e2(1) =0.0, e2(2)=1.0, e2(3) = 0.0, nx=20, ny=20 & -------------------------------------------------------------------------------- and the error is : -------------------------------------------------------------------------------- nbndx = 40 nbnd = 40 natomwfc = 66 npwx = 23472 nelec = 66.00 nkb = 132 ngl = 13548 Calling punch_plot, plot_num = 7 IOS = ** %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from davcio : error # 10 i/o error in davcio %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... -------------------------------------------------------------------------------- Thanks for your help. Yours, Ma -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061213/9dbfaa38/attachment.htm From yuwen_66 at yahoo.com Wed Dec 13 05:36:57 2006 From: yuwen_66 at yahoo.com (W. YU) Date: Tue, 12 Dec 2006 20:36:57 -0800 (PST) Subject: [Pw_forum] what's wrong with 'nscf' when doing bands? Message-ID: <645144.90853.qm@web51009.mail.yahoo.com> Dear Stefano, Thank you very much for answering my question. >you should not specify calculation='nscf' but >calculation='bands' for >band structure run. The above suggestion really works for my case. But I am at a lost. I have been using 'nscf' for band structure calculation for a very long time and found no error at all. BTW, I found 'nscf' and 'bands' key words mixed in the examples of espresso 3.1.1 for band structure calculation. Examples05 use 'nscf' while example01 use 'bands'. Both works. Then what is the difference between these? If we must use 'bands' for band structure, when do we need 'nscf' or it is obsolete? best regards, Wen Yu ____________________________________________________________________________________ Need a quick answer? Get one in minutes from people who know. Ask your question on www.Answers.yahoo.com From amit76.india at gmail.com Wed Dec 13 07:06:43 2006 From: amit76.india at gmail.com (Amit Kumar) Date: Wed, 13 Dec 2006 11:36:43 +0530 Subject: [Pw_forum] El-ph coupling Lambda Message-ID: Respected Users, Following Prof. Axel's recommendation, I first went through the source code lambda,f90. Then I tried to compile it separately. I'm getting the following error : ifort lambda.f90 -o lambda.x /tmp/ifort8HJdyc.o(.text+0x669): In function `MAIN__': : undefined reference to `errore_' /tmp/ifort8HJdyc.o(.text+0x741): In function `MAIN__': : undefined reference to `errore_' /tmp/ifort8HJdyc.o(.text+0x933): In function `MAIN__': : undefined reference to `w0gauss_' /tmp/ifort8HJdyc.o(.text+0xfb9): In function `MAIN__': : undefined reference to `errore_' /tmp/ifort8HJdyc.o(.text+0x1040): In function `MAIN__': : undefined reference to `errore_' /tmp/ifort8HJdyc.o(.text+0x1067): In function `MAIN__': : undefined reference to `errore_' /tmp/ifort8HJdyc.o(.text+0x108a): In function `MAIN__': : undefined reference to `errore_' /tmp/ifort8HJdyc.o(.text+0x10aa): In function `MAIN__': : undefined reference to `errore_' I see lambda.f90 is calling a module errore. But I'm not finding errore anywhere. I'll be highly obliged if someone help me to get lambda.x from lambda.f90and give some clue for calculating the el-ph coupling in a magnetic metal (say Nickel). Looking forward to your kind reply. Regards, Amit >>>>>>>>>>if you feel ready to program something, you should check out the development cvs. How shall I check it??? I'm unable to connect. Here is the problem. cvs login Logging in to :pserver:cvsanon at democritos.sissa.it:2401/home/cvs CVS password: cvs [login aborted]: connect to democritos.sissa.it(147.122.10.31):2401 failed: Connection timed out -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061213/42c14d51/attachment.htm From degironc at sissa.it Wed Dec 13 09:10:11 2006 From: degironc at sissa.it (degironc) Date: Wed, 13 Dec 2006 09:10:11 +0100 Subject: [Pw_forum] what's wrong with 'nscf' when doing bands? In-Reply-To: <645144.90853.qm@web51009.mail.yahoo.com> References: <645144.90853.qm@web51009.mail.yahoo.com> Message-ID: <457FB563.4050208@sissa.it> W. YU wrote: >Dear Stefano, > >Thank you very much for answering my question. > > > >>you should not specify calculation='nscf' but >>calculation='bands' for >>band structure run. >> >> >The above suggestion really works for my case. But I >am at a lost. I have been using 'nscf' for band >structure calculation for a very long time and found >no error at all. BTW, I found 'nscf' and 'bands' key >words mixed in the examples of espresso 3.1.1 for band >structure calculation. Examples05 use 'nscf' while >example01 use 'bands'. Both works. Then what is the >difference between these? If we must use 'bands' for >band structure, when do we need 'nscf' or it is >obsolete? > > I agree that is it confusing but the problem is that in the case you declare a metallic system 'nscf' try to locate the Fermi energy which is meaningless for a band structure calculation (in particular when kpoints have zero weight as in your input...) while 'bands' does not. 'nscf' was in the past the only option for a non-scf calculation and this has been in the past a source of problems because it was used for 1) band structure calculation, 2) BZ refining in order to obtain nicer dos etc, and 3) preparation-run for phonon calculations and maybe other uses as well... The needs of these different types of calculation are different... 1) does not need any occupation number, k-poit sampling and weight should be totally arbitrary and not changed internally while 2) and 3) reguire and even sampling of the BZ which takes into consideration reduction of symmetry w.r.t. the declared bravais lattice , and 3) should be made, to be consistent, with exactly the same sampling as the original scf calculation... These competing needs call for specific key-values. NOW calculation variable has specific keys-values for 'bands' and 'phonon' but still a generic 'nscf'' value which, as I said, in metallic calculations try to locate the Fermi energy and create the problem you reported. For non metallic systems all these options are probably equivalent or at least nscf and bands are hence the (lousy) use of 'nscf' in examples as 'bands' replacement. Hope this clarify but I'm sure this issue will reappear in the forum in the future... best regards, stefano >best regards, > >Wen Yu > > > >____________________________________________________________________________________ >Need a quick answer? Get one in minutes from people who know. >Ask your question on www.Answers.yahoo.com >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > From giannozz at nest.sns.it Wed Dec 13 09:13:08 2006 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 13 Dec 2006 09:13:08 +0100 Subject: [Pw_forum] problems using pp.x In-Reply-To: References: Message-ID: <3EBB7FC4-0B02-4802-9F03-9EBBFAE676D2@nest.sns.it> On Dec 13, 2006, at 4:00 , Fengjie Ma wrote: > When I used pp.x to analyse and plot data after "scf" and "nscf", I > met some problems > [...] > from davcio : error # 10 > i/o error in davcio the data file is not there or is not complete Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From fengjie.ma at gmail.com Wed Dec 13 10:56:43 2006 From: fengjie.ma at gmail.com (Fengjie Ma) Date: Wed, 13 Dec 2006 17:56:43 +0800 Subject: [Pw_forum] Re: problems using pp.x Message-ID: Hi Paolo, But when I set plot_num = 0 or plot_num = 6, it works ok. And I don't delete any products of "scf" and "nscf" like "*.wfc", "*.pot", "*.rho" and "*.save". Yours, Ma -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061213/583f313b/attachment.htm From babazade at gmail.com Wed Dec 13 13:09:54 2006 From: babazade at gmail.com (Amin Babazadeh) Date: Wed, 13 Dec 2006 15:39:54 +0330 Subject: [Pw_forum] permittivity In-Reply-To: References: Message-ID: Dear Andrea Sorry for getting your time.I look at the document that you recommend me and then i try to calculate epsilon but i couldn't find epsilon.x. i only find the epsilon.f90.Should i compile epsilon.f90?i think when we compiled the espresso all of the code has been installed. thanks a lot amin On 12/12/06, Andrea Ferretti wrote: > > > > On Tue, 12 Dec 2006, Amin Babazadeh wrote: > > > dear users > > I work with quantum espresso code and i want to know if we can find > optical > > properties (permittivity, susceptibility, absorption,....) with using > this > > cod. > > i search in the examples but i couldn't;t find any thing. > > i will appreciate your help > > > > in the last release of espresso (v3.2) you can find the program > PP/epsilon.f90: > this is a simple code for the computation of optical properties > (basically absorption) at the RPA > level on the kohn-sham electronic structure, without the inclusion of > local fields. The methods implemented and the input file are more or less > described in Doc/eps_man.tex > > andrea > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- AMIN -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061213/a2d32b2e/attachment.htm From akohlmey at cmm.chem.upenn.edu Wed Dec 13 16:44:01 2006 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 13 Dec 2006 10:44:01 -0500 (EST) Subject: [Pw_forum] El-ph coupling Lambda In-Reply-To: Message-ID: On Wed, 13 Dec 2006, Amit Kumar wrote: AK> Respected Users, AK> AK> Following Prof. Axel's recommendation, I first went through the source AK> code AK> lambda,f90. Then I tried to compile it separately. amit, i meant to read through more than just the one file. you should get a feeling for what is stored/handled where, what kind of subroutine is put in what subdirectory, how to import/re-use existing functionality, what style of programming to use and where and how you'd add new functionality. if you _were_ acquainted with the code and how everything within QE is structured, you would not stumble over this (trivial) issue. getting to know a big package code can take a while (not just a couple of hours). but please read on. AK> I'm getting the following error : AK> AK> ifort lambda.f90 -o lambda.x AK> /tmp/ifort8HJdyc.o(.text+0x669): In function `MAIN__': AK> : undefined reference to `errore_' AK> /tmp/ifort8HJdyc.o(.text+0x741): In function `MAIN__': AK> : undefined reference to `errore_' AK> /tmp/ifort8HJdyc.o(.text+0x933): In function `MAIN__': AK> : undefined reference to `w0gauss_' AK> /tmp/ifort8HJdyc.o(.text+0xfb9): In function `MAIN__': AK> : undefined reference to `errore_' AK> /tmp/ifort8HJdyc.o(.text+0x1040): In function `MAIN__': AK> : undefined reference to `errore_' AK> /tmp/ifort8HJdyc.o(.text+0x1067): In function `MAIN__': AK> : undefined reference to `errore_' AK> /tmp/ifort8HJdyc.o(.text+0x108a): In function `MAIN__': AK> : undefined reference to `errore_' AK> /tmp/ifort8HJdyc.o(.text+0x10aa): In function `MAIN__': AK> : undefined reference to `errore_' AK> AK> I see lambda.f90 is calling a module errore. AK> But I'm not finding errore anywhere. it is defined in flib/error.f90 this subroutine serves as common interface to have serial and especially parallel runs stop cleanly (programs within QE, except for small serial utility programs must not use STOP to terminate). the simplest way of finding where a fortran subroutine is defined in QE is to go to the toplevel directory and, e.g., do a: grep -i errore */*.f* | grep -i subroutine since the lambda.x code does not (re-)use any other existing methods it is probably best, you include a stripped down serial version of that subroutine. other than that, you can just add ../flib/flib.a to the list of object to link to lambda.x. AK> I'll be highly obliged if someone help me to get lambda.x from lambda.f90and AK> give some clue for calculating the el-ph coupling in a magnetic metal (say AK> Nickel). i strongly suggest, you first work on understand the technical issues involved, make notes on how the flow of data is handled currently, try to understand what the individual step of the calculation in the code are and _then_ come back and discuss what kind of changes you would suggest to implement. it is always better to first start with a problem that you know the answer to before you jump the gun and go to more challenging tasks. cheers, axel. AK> AK> Looking forward to your kind reply. AK> AK> Regards, AK> Amit AK> AK> AK> AK> >>>>>>>>>>if you feel ready to program something, you should check out the AK> development AK> cvs. AK> AK> How shall I check it??? AK> I'm unable to connect. AK> AK> Here is the problem. AK> AK> cvs login AK> Logging in to :pserver:cvsanon at democritos.sissa.it:2401/home/cvs AK> CVS password: AK> cvs [login aborted]: connect to democritos.sissa.it(147.122.10.31):2401 AK> failed: Connection timed out AK> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From ferretti.andrea at unimore.it Wed Dec 13 17:14:16 2006 From: ferretti.andrea at unimore.it (Andrea Ferretti) Date: Wed, 13 Dec 2006 17:14:16 +0100 (CET) Subject: [Pw_forum] permittivity In-Reply-To: References: Message-ID: Dear Amin, as far as I remember, epsilon.x is not compiled by default (e.g by make all or make pp) instead, you should enter the PP directory and type make epsilon.x this is because this code is still experimental and little tested andrea > Dear Andrea > Sorry for getting your time.I look at the document that you recommend me and > then i try to calculate epsilon but i couldn't find epsilon.x. > i only find the epsilon.f90.Should i compile epsilon.f90?i think when we > compiled the espresso all of the code has been installed. > thanks a lot > amin > From giannozz at nest.sns.it Wed Dec 13 17:42:03 2006 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 13 Dec 2006 17:42:03 +0100 Subject: [Pw_forum] Re: problems using pp.x In-Reply-To: References: Message-ID: <09C3E94C-607C-4BCD-9997-853AA9177143@nest.sns.it> On Dec 13, 2006, at 10:56 , Fengjie Ma wrote: > But when I set plot_num = 0 or plot_num = 6, it works ok. > And I don't delete any products of "scf" and "nscf" like > "*.wfc", "*.pot", "*.rho" and "*.save". it works for me --- Paolo Giannozzi, Democritos and University of Udine, Italy From amit76.india at gmail.com Wed Dec 13 19:23:29 2006 From: amit76.india at gmail.com (Amit Kumar) Date: Wed, 13 Dec 2006 23:53:29 +0530 Subject: [Pw_forum] from elphsum : error # 3 Message-ID: Respected Users, I'm getting the following error during the electron phonon calculation. electron-phonon interaction ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from elphsum : error # 3 q is not a vector in the dense grid %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... Could anyone tell me what might be the possible reason of this error??? Should I use 16x16x16 MP grid for q points instead of 4x4x4 grids to get rid of the above error???? Regards, Amit -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061213/fbb84688/attachment.htm From wierzbom at ts.infn.it Wed Dec 13 20:03:22 2006 From: wierzbom at ts.infn.it (Malgorzata Wierzbowska) Date: Wed, 13 Dec 2006 20:03:22 +0100 (CET) Subject: [Pw_forum] from elphsum : error # 3 In-Reply-To: References: Message-ID: On Wed, 13 Dec 2006, Amit Kumar wrote: The error below shows up in elphon.f90 when the q-vectors are NOT a SUBSET of the K_POINTS grid which is defined in the scf run with la2F = .true. Gosia > Respected Users, > > > I'm getting the following error during the electron phonon calculation. > > electron-phonon interaction ... > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from elphsum : error # 3 > q is not a vector in the dense grid > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > > > Could anyone tell me what might be the possible reason of this error??? > > Should I use 16x16x16 MP grid for q points instead of 4x4x4 grids to > get rid of the above error???? > > Regards, > Amit > From naivebamboo at hotmail.com Thu Dec 14 04:27:14 2006 From: naivebamboo at hotmail.com (naivebamboo Huang) Date: Wed, 13 Dec 2006 22:27:14 -0500 Subject: [Pw_forum] Specify the states to be pseudized Message-ID: Dear PWscf users, This is my first time to use pseudopotential DFT. I downloaded the PBE pseudopotential for Bi from abinit website and tried to convert it to UPF format. When I run fhi2upf.x, I was asked to input "label, occupancy" . I don't know how to do that because I know little about the details of pseudopotential. The 83-Bi.GGA.ini for FHI code is attached at the end of this mail. Would anyone please tell me how to choose "label, occupancy" (4 wavefunctions) from the .ini file? The output of FHI code also have the following comments: bismuth, fhi98PP : Trouiller-Martins-type, GGA Perdew/Burke/Ernzerhof (1996), l= 0 local 83.000 5.000 011001 zatom,zion,pspdat 6 11 3 0 569 0 pspcod,pspxc,lmax,lloc,mmax,r2well 6.691 1.000 0.000 rchrg, fchrg, qchrg Another related question is how to specify the states to be pseudized in ld1.x. Label N L Occupancy energy Ecut US Rcut Can I specify all of these parameter according to the .ini file of fhi98pp? If I don't have the .ini file, how can I specify them? (that is, how to determine which state shoud be pseudized and how to specify the values of energy, Ecut and US Rcut?) Thanks very much Baoling Huang 83.00 13 2 6 1.30 : z nc nv 1 0 2.00 : n l f 2 0 2.00 2 1 6.00 3 0 2.00 3 1 6.00 3 2 10.00 4 0 2.00 4 1 6.00 4 2 10.00 4 3 14.00 5 0 2.00 5 1 6.00 5 2 10.00 6 0 2.00 6 1 3.00 3 "t" : lmax s_pp_def 2 0.0 10.00 "t" 0 3.806 0 "t" 1 0.0 0 "t" 3 0.0 0.01 "t" _________________________________________________________________ Get free, personalized commercial-free online radio with MSN Radio powered by Pandora http://radio.msn.com/?icid=T002MSN03A07001 From yuwen_66 at yahoo.com Thu Dec 14 06:45:32 2006 From: yuwen_66 at yahoo.com (W. YU) Date: Wed, 13 Dec 2006 21:45:32 -0800 (PST) Subject: [Pw_forum] further questions about 'nscf' and system control in 'nscf' Message-ID: <85806.67615.qm@web51013.mail.yahoo.com> Thanks Stefano, Now some other questions have come to my mind: >'nscf' was in the past the only option for a non-scf >calculation and >this has been in the past a source of >problems because it was used for 1) band structure >calculation, 2) BZ >refining in order to obtain nicer >dos etc, and 3) preparation-run for phonon >calculations and maybe other >uses as well... ==================================================== >The needs of these different types of calculation >are different... and 3) should be made, to be >consistent, >with exactly the same sampling >as the original scf calculation... Does this mean the k-point grid for 'phonon' calculation should ALWAYS (at least in principle) be the same as the 'scf' part? If so, what will happen if it is not? Now this also reminds me of questions about general setup of SYSTEM control and K_POINTS for nscf calculations including 'phonon','bands', and 'nscf'. This is how I understant it: ==== 1. The ecut and ecutrho could be different from the scf part concerning all the three nscf calculations,even the smearing method and parameters supplied when dealing with a metallic system. 2. The k-points can and really should be different for band and dos type calculations. For phonon, I am not sure,I need your confirmation. 3. If it is a spin-polarized calculation, if I already set the starting_magnetization say equals 0.5, why should I set it again in the band and other nscf calculation since the selfconsistency is already achieved and the magnetization is determined by the scf cycle. Best wishes, Wen YU ====================================================== ____________________________________________________________________________________ Cheap talk? Check out Yahoo! Messenger's low PC-to-Phone call rates. http://voice.yahoo.com From babazade at gmail.com Thu Dec 14 08:37:33 2006 From: babazade at gmail.com (Amin Babazadeh) Date: Thu, 14 Dec 2006 11:07:33 +0330 Subject: [Pw_forum] permittivity In-Reply-To: References: Message-ID: Dear Andrea Thanks a lot for your help.I did your recommendation. Sincerely yours amin On 12/13/06, Andrea Ferretti wrote: > > > Dear Amin, > > as far as I remember, epsilon.x is not compiled by default (e.g by make > all or make pp) > instead, you should enter the PP directory and type > make epsilon.x > > this is because this code is still experimental and little tested > > andrea > > > > Dear Andrea > > Sorry for getting your time.I look at the document that you recommend me > and > > then i try to calculate epsilon but i couldn't find epsilon.x. > > i only find the epsilon.f90.Should i compile epsilon.f90?i think when we > > compiled the espresso all of the code has been installed. > > thanks a lot > > amin > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- AMIN -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061214/1637b488/attachment.htm From chen_shao_hua197 at yahoo.com.tw Thu Dec 14 09:16:07 2006 From: chen_shao_hua197 at yahoo.com.tw (=?big5?q?=B3=AF=20=A4=D6=B5=D8?=) Date: Thu, 14 Dec 2006 16:16:07 +0800 (CST) Subject: [Pw_forum] Can we calculate the el-ph coulping by US PPs ? Message-ID: <410472.29150.qm@web73007.mail.tp2.yahoo.com> Dear users, I thought a paper(Nature Vol 444 | 23),mentioned about their Ab initio calculation of el-ph coulping by Pwscf. It is in the latest paragraph of article. It says " Our calculations were based on an ultrasoft pseudopotential plane-wave implementation of density functional theory with a generalized-gradient description of the exchange-correlation functional. They were performed with the Plane Wave Self-Consistent Field package (www.pwscf.org) ". What I wonder is according to Pwscf PP's homepage. It says "Note however that calculations of effective charges, electron-phonon coefficients, third-order derivatives are not implemented with US PPs." So who is wrong ? Can we calculate the el-ph coulping by US PPs ? Best Regards Max ___________________________________________________ ??????? ? ???????????????? http://messenger.yahoo.com.tw/ From degironc at sissa.it Thu Dec 14 09:36:27 2006 From: degironc at sissa.it (degironc) Date: Thu, 14 Dec 2006 09:36:27 +0100 Subject: [Pw_forum] Can we calculate the el-ph coulping by US PPs ? In-Reply-To: <410472.29150.qm@web73007.mail.tp2.yahoo.com> References: <410472.29150.qm@web73007.mail.tp2.yahoo.com> Message-ID: <45810D0B.2010701@sissa.it> effective charges and el-ph coefficients using US PP have been implemented (one or two years ago) while third-order coefficients are not available (and no one is working on that to my knowledge). Thanks for pointing us the inconsistensy in the web page. stefano ? ?? wrote: >Dear users, >I thought a paper(Nature Vol 444 | 23),mentioned about >their Ab initio calculation of el-ph coulping by >Pwscf. It is in the latest paragraph of article. > >It says " Our calculations were based on an ultrasoft >pseudopotential plane-wave implementation of density >functional theory with a generalized-gradient >description of the exchange-correlation functional. >They were performed with the Plane Wave >Self-Consistent Field package (www.pwscf.org) ". > >What I wonder is according to Pwscf PP's homepage. >It says "Note however that calculations of effective >charges, electron-phonon coefficients, third-order >derivatives are not implemented with US PPs." > >So who is wrong ? Can we calculate the el-ph coulping >by US PPs ? > >Best Regards >Max > >___________________________________________________ > ??????? ? ???????????????? > http://messenger.yahoo.com.tw/ >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > From giannozz at nest.sns.it Thu Dec 14 10:52:49 2006 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 14 Dec 2006 10:52:49 +0100 Subject: [Pw_forum] Specify the states to be pseudized In-Reply-To: References: Message-ID: <57B44F22-AEB5-4540-82CD-1002D4039B25@nest.sns.it> On Dec 14, 2006, at 4:27 , naivebamboo Huang wrote: > I downloaded the PBE pseudopotential for Bi from abinit website > and tried to convert it to UPF format. When I run fhi2upf.x, I was > asked to input "label, occupancy" . I don't know how to do that > because I know little about the details of pseudopotential. but you should know that the Bi atom has [Xe] 4f14 5d10 6s2 6p3 electronic configuration, so the labels and occupancies of the valence states are 6s and 2, 6p and 3, presumably > Another related question is how to specify the states to be pseudized > in ld1.x it is explained in detail in the documentation (atomic_doc/) Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From chen_shao_hua197 at yahoo.com.tw Thu Dec 14 11:30:48 2006 From: chen_shao_hua197 at yahoo.com.tw (=?big5?q?=B3=AF=20=A4=D6=B5=D8?=) Date: Thu, 14 Dec 2006 18:30:48 +0800 (CST) Subject: [Pw_forum] what negative omiga means ? Message-ID: <224900.66712.qm@web73013.mail.tp2.yahoo.com> Dear members, I have a little question bothering me.After I calculated the phonon dispersion. I got some negative omiga values. As I know ,image omiga means unstable.But what negative omiga means ? I suppose it should be positive value,if it is stable system. Best Regards max ___________________________________________________ ??????? ? ???????????????? http://messenger.yahoo.com.tw/ From degironc at sissa.it Thu Dec 14 11:41:17 2006 From: degironc at sissa.it (degironc) Date: Thu, 14 Dec 2006 11:41:17 +0100 Subject: [Pw_forum] further questions about 'nscf' and system control in 'nscf' In-Reply-To: <85806.67615.qm@web51013.mail.yahoo.com> References: <85806.67615.qm@web51013.mail.yahoo.com> Message-ID: <45812A4D.4020504@sissa.it> W. YU wrote: >Thanks Stefano, > >Now some other questions have come to my mind: > > > >>'nscf' was in the past the only option for a non-scf >>calculation and >>this has been in the past a source of >>problems because it was used for 1) band structure >>calculation, 2) BZ >>refining in order to obtain nicer >>dos etc, and 3) preparation-run for phonon >>calculations and maybe other >>uses as well... >> >> >==================================================== > > >>The needs of these different types of calculation >>are different... and 3) should be made, to be >>consistent, >>with exactly the same sampling >>as the original scf calculation... >> >> > >Does this mean the k-point grid for 'phonon' >calculation should ALWAYS (at least in principle) be >the same as the 'scf' part? If so, what will happen if >it is not? > > 'phonon' flag should be used with exactly the same grid that generated the scf potential... Its aim is to generate the SAME unperturbed information on the k and k+q points that are needed for the linear response calculation... In the past there was a check that the newly calculated charge density agreed with the scf one... now I think this check has got lost but we should reintroduce it. >Now this also reminds me of questions about general >setup of SYSTEM control and K_POINTS for nscf >calculations including 'phonon','bands', and 'nscf'. > >This is how I understant it: >==== >1. The ecut and ecutrho could be different from the >scf part concerning all the three nscf >calculations,even the smearing method and parameters >supplied when dealing with a metallic system. > > I think that ecut and ecutrho should be kept the same as in the nscf/lband/phonon case the scf density and potential are read from files into arrays with dimensions determined on the basis of those numbers. smearing parameteres should be irrelevant for bands as the potential is fixed and no occupation is calculated... for the phonon case one should be consistent... for the nscf case I think one can experiment with these features knowing that the resulting charge density or dos will be slightly inconsistent. >2. The k-points can and really should be different for >band and dos type calculations. For phonon, I am not >sure,I need your confirmation. > > As I said above the phonon calculation should really be the same as the scf calculation plus the indication of the desired q vector. >3. If it is a spin-polarized calculation, if I already >set the starting_magnetization say equals 0.5, why >should I set it again in the band and other nscf >calculation since the selfconsistency is already >achieved and the magnetization is determined by the >scf cycle. > > The code check this quanties even if they are not needed in a nscf calculation or in a restart from previously interrupted run. The code is not using this information in tese cases. The problem in this "illogical" behavior is the number of special cases that one should keep in mind when trying to make it more logical. best wishes, stefano >Best wishes, > >Wen YU >====================================================== >____________________________________________________________________________________ >Cheap talk? >Check out Yahoo! Messenger's low PC-to-Phone call rates. >http://voice.yahoo.com >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > From degironc at sissa.it Thu Dec 14 11:42:57 2006 From: degironc at sissa.it (degironc) Date: Thu, 14 Dec 2006 11:42:57 +0100 Subject: [Pw_forum] what negative omiga means ? In-Reply-To: <224900.66712.qm@web73013.mail.tp2.yahoo.com> References: <224900.66712.qm@web73013.mail.tp2.yahoo.com> Message-ID: <45812AB1.2020508@sissa.it> when omega^2 is negative the code prints - sqrt(abs(omega^2)) stefano ? ?? wrote: >Dear members, >I have a little question bothering me.After I >calculated the phonon dispersion. I got some negative >omiga values. >As I know ,image omiga means unstable.But what >negative omiga means ? I suppose it should be positive >value,if it is stable system. > >Best Regards >max > >___________________________________________________ > ??????? ? ???????????????? > http://messenger.yahoo.com.tw/ >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > From babazade at gmail.com Thu Dec 14 12:12:21 2006 From: babazade at gmail.com (Amin Babazadeh) Date: Thu, 14 Dec 2006 14:42:21 +0330 Subject: [Pw_forum] about epsilon Message-ID: dear users I want to find optical properties of ZnS so i used epsilon.x for doing it.but this error has been written. Program POST-PROC v.3.2 starts ... Today is 14Dec2006 at 13:53: 7 nbndx = 13 nbnd = 13 natomwfc = 15 npwx = 1056 nelec = 18.00 nkb = 24 ngl = 134 Check: negative/imaginary core charge= -0.000067 0.000000 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from epsilon : error # 1 USPP are not implemented %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... i think this error says that the epsilon.x doesn't work on US pseudopotential but i am not sure so i look at the epsilon.f90 in that file it was written: ----- ----- USE uspp, ONLY : okvan ------ ------ IF ( okvan ) CALL errore('epsilon','USPP are not implemented',1) ------ i don't know what okvan is?is this mean a spatial kind of USPP i should use or it said that i can't use US pseudopotential. I also want to test it with non conserving potential bur unfortunately i couldn't find any pseudopotential for ZnS.would you please help me and tell me what should i do? I will appreciate your help. sincerely yours amin -- AMIN -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061214/4612fbd5/attachment.htm From ferretti.andrea at unimore.it Thu Dec 14 12:54:33 2006 From: ferretti.andrea at unimore.it (Andrea Ferretti) Date: Thu, 14 Dec 2006 12:54:33 +0100 (CET) Subject: [Pw_forum] about epsilon In-Reply-To: References: Message-ID: > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from epsilon : error # 1 > USPP are not implemented > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > i think this error says that the epsilon.x doesn't work on US > pseudopotential this is exactly the point, you are right... > ------ > IF ( okvan ) CALL errore('epsilon','USPP are not implemented',1) > ------ > i don't know what okvan is?is this mean a spatial kind of USPP i should use > or it said that i can't use US pseudopotential. okwan is a logical variable which is .TRUE. if at least one of the pseudopotentials in the calculation is ultrasoft (or vanderbilt type)... > I also want to test it with non conserving potential bur unfortunately i > couldn't find any pseudopotential for ZnS. unfortunately, while S does not need USPP, Zn is it quite hard in terms of cutoff energy, and therefore, after a brief check, it seems the pseudopage of espresso does not contain any norm-conserving pseudo for Zn. andrea From babazade at gmail.com Thu Dec 14 13:10:58 2006 From: babazade at gmail.com (Amin Babazadeh) Date: Thu, 14 Dec 2006 15:40:58 +0330 Subject: [Pw_forum] about epsilon In-Reply-To: References: Message-ID: Dear Andrea Thanks a lot for your clear answer. I have another question.do you have a any idea for solving my problem i will appreciate if you give me some idea. can i find pseudopotential from other cods like abinit?I didn't work with abinit or it's pseudopotentail but i see in the espresso's mailing list that some people use the abinit pseudopotentail. thanks a lot On 12/14/06, Andrea Ferretti wrote: > > > > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > from epsilon : error # 1 > > USPP are not implemented > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > > > i think this error says that the epsilon.x doesn't work on US > > pseudopotential > > this is exactly the point, you are right... > > > ------ > > IF ( okvan ) CALL errore('epsilon','USPP are not implemented',1) > > ------ > > i don't know what okvan is?is this mean a spatial kind of USPP i should > use > > or it said that i can't use US pseudopotential. > > okwan is a logical variable which is .TRUE. if at least one of the > pseudopotentials in the calculation is ultrasoft (or vanderbilt type)... > > > > I also want to test it with non conserving potential bur > unfortunately i > > couldn't find any pseudopotential for ZnS. > > unfortunately, while S does not need USPP, Zn is it quite hard in terms of > cutoff energy, and therefore, after a brief check, it seems the pseudopage > of espresso does not contain any norm-conserving pseudo for Zn. > > andrea > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- AMIN -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061214/641b018d/attachment.htm From chen_shao_hua197 at yahoo.com.tw Thu Dec 14 13:16:17 2006 From: chen_shao_hua197 at yahoo.com.tw (=?big5?q?=B3=AF=20=A4=D6=B5=D8?=) Date: Thu, 14 Dec 2006 20:16:17 +0800 (CST) Subject: [Pw_forum] what negative omiga means ? In-Reply-To: <45812AB1.2020508@sissa.it> Message-ID: <631019.74861.qm@web73011.mail.tp2.yahoo.com> I see ,thank you very much. max --- degironc ?? > when omega^2 is negative the code prints - > sqrt(abs(omega^2)) > stefano > > ? ?? wrote: > > >Dear members, > >I have a little question bothering me.After I > >calculated the phonon dispersion. I got some > negative > >omiga values. > >As I know ,image omiga means unstable.But what > >negative omiga means ? I suppose it should be > positive > >value,if it is stable system. > > > >Best Regards > >max > > > >___________________________________________________ > > > ??????? ? ???????????????? > > > http://messenger.yahoo.com.tw/ > >_______________________________________________ > >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 > ___________________________________________________ ??????? ? ???????????????? http://messenger.yahoo.com.tw/ From degironc at sissa.it Thu Dec 14 13:47:25 2006 From: degironc at sissa.it (degironc) Date: Thu, 14 Dec 2006 13:47:25 +0100 Subject: [Pw_forum] about epsilon In-Reply-To: References: Message-ID: <458147DD.8030700@sissa.it> Dear Amin, using US PP would be preferable but if this is not possible one option is to use a Zn pseudopotential that bury the 3d orbital in the core. You NEED THEN to use non-linear core correction in the pseudopotential otherwise very poor results are obtained but with NLCC some decent description comes out for semiconductors [see for instance Ferroelectrics 111, 19 (1990); Phys. Rev. B 47, 3588 (1993), Phys. Rev. Lett. 80, 4939 (1998), Appl. Phys. Lett. 75, 2746 (1999) ]. Unfortunately I don't have at hand any of the Zn pseudopotentials used in those works... I ll' try to dig in my archives but you may also try to generate one using ld1.x code (maybe modifying the input for As or the one for Al that are included in atomoc_doc/pseudo-gen/ ... ) stefano Amin Babazadeh wrote: > Dear Andrea > Thanks a lot for your clear answer. > I have another question.do you have a any idea for solving my problem > i will appreciate if you give me some idea. > can i find pseudopotential from other cods like abinit?I didn't work > with abinit or it's pseudopotentail but i see in the espresso's > mailing list that some people use the abinit pseudopotentail. > thanks a lot > > On 12/14/06, *Andrea Ferretti* > wrote: > > > > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > from epsilon : error # 1 > > USPP are not implemented > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > > > > i think this error says that the epsilon.x doesn't work on US > > pseudopotential > > this is exactly the point, you are right... > > > ------ > > IF ( okvan ) CALL errore('epsilon','USPP are not implemented',1) > > ------ > > i don't know what okvan is?is this mean a spatial kind of USPP i > should use > > or it said that i can't use US pseudopotential. > > okwan is a logical variable which is .TRUE. if at least one of the > pseudopotentials in the calculation is ultrasoft (or vanderbilt > type)... > > > > I also want to test it with non conserving potential bur > unfortunately i > > couldn't find any pseudopotential for ZnS. > > unfortunately, while S does not need USPP, Zn is it quite hard in > terms of > cutoff energy, and therefore, after a brief check, it seems the > pseudopage > of espresso does not contain any norm-conserving pseudo for Zn. > > andrea > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > AMIN From chen_shao_hua197 at yahoo.com.tw Thu Dec 14 14:40:09 2006 From: chen_shao_hua197 at yahoo.com.tw (=?big5?q?=B3=AF=20=A4=D6=B5=D8?=) Date: Thu, 14 Dec 2006 21:40:09 +0800 (CST) Subject: [Pw_forum] Can ph.x be executed parallelly ? Message-ID: <898137.11410.qm@web73014.mail.tp2.yahoo.com> Dear members, I had compiled the MPI version of QE 3.0 successfully.I runned it in PC clusters.If I used >1 nodes ,I can see pw.x executed in those nodes.But I can't see ph.x executed in two or more nodes,it just executed in single one node (or CPU). Is it my PBS systen problem or ph.x can't be runned parallelly ? If it is latter factor,then it means phonon and el-ph coulping can't be runned parallelly ? Best Regards Max ___________________________________________________ ??????? ? ???????????????? http://messenger.yahoo.com.tw/ From srijan.india at gmail.com Thu Dec 14 14:42:50 2006 From: srijan.india at gmail.com (Srijan Kumar Saha) Date: Thu, 14 Dec 2006 19:12:50 +0530 Subject: [Pw_forum] compilation error In-Reply-To: References: <3fcc7e670612120605r36efeb98pe0309b084cfa6957@mail.gmail.com> Message-ID: <3fcc7e670612140542v13b5e572s828731e844ae74db@mail.gmail.com> Respected Users, I have changed the previous ifort compiler. Now I'm getting the following error. configure: success /espresso-3.2 > make all test -d bin || mkdir bin if test -d iotk ; then \ ( cd iotk ; if test "make" = "" ; then make TLDEPS= libiotk.a ; \ else make TLDEPS= libiotk.a ; fi ) ; fi make[1]: Entering directory `/home/espresso-3.2/iotk' cd src ; make libiotk.a make[2]: Entering directory `/home/espresso-3.2/iotk/src' mpif90 -O2 -tpp6 -assume byterecl -nomodule -fpp -D__INTEL -D__FFTW -D__USE_INTERNAL_FFTW -I../include -lfftw -I./ -I../Modules -I../iotk/src -I../PW -I../PH -I../CPV -c iotk_base.f90 /hpc/mpich/bin/mpif90: line 332: eval: -O: invalid option eval: usage: eval [arg ...] make[2]: *** [iotk_base.o] Error 2 make[2]: Leaving directory `/home/espresso-3.2/iotk/src' make[1]: *** [libiotk.a] Error 2 make[1]: Leaving directory `/home/espresso-3.2/iotk' make: *** [libiotk] Error 2 What does the above error mean? How to solve this problem? With best regards, Srijan -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061214/b66e4429/attachment.htm From chen_shao_hua197 at yahoo.com.tw Thu Dec 14 14:51:59 2006 From: chen_shao_hua197 at yahoo.com.tw (=?big5?q?=B3=AF=20=A4=D6=B5=D8?=) Date: Thu, 14 Dec 2006 21:51:59 +0800 (CST) Subject: [Pw_forum] the error message which I can not recognized. Message-ID: <847567.73573.qm@web73001.mail.tp2.yahoo.com> Dear members, When I runned phonon dispersion ,the end of output file below showed the error message which I can not recognized. nbndx = 12 nbnd = 12 natomwfc = 16 npwx = 233 nelec = 16.00 nkb = 10 ngl = 390 starting from an old run Doing now the calculation for q point nr 1 ** ON ENTRY TO ZHPEV PARAMETER NUMBER 1 HAD AN ILLEGAL VALUE Can anyone tell me how should I fixed the error ? Thank you very much !! Max ___________________________________________________ ??????? ? ???????????????? http://messenger.yahoo.com.tw/ From giannozz at nest.sns.it Thu Dec 14 14:53:48 2006 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 14 Dec 2006 14:53:48 +0100 Subject: [Pw_forum] Can ph.x be executed parallelly ? In-Reply-To: <898137.11410.qm@web73014.mail.tp2.yahoo.com> References: <898137.11410.qm@web73014.mail.tp2.yahoo.com> Message-ID: <9B82D8B4-C332-4C47-B1FC-392D83049DA7@nest.sns.it> yes --- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at nest.sns.it Thu Dec 14 14:55:36 2006 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 14 Dec 2006 14:55:36 +0100 Subject: [Pw_forum] compilation error In-Reply-To: <3fcc7e670612140542v13b5e572s828731e844ae74db@mail.gmail.com> References: <3fcc7e670612120605r36efeb98pe0309b084cfa6957@mail.gmail.com> <3fcc7e670612140542v13b5e572s828731e844ae74db@mail.gmail.com> Message-ID: On Dec 14, 2006, at 14:42 , Srijan Kumar Saha wrote: > > mpif90 -O2 -tpp6 -assume byterecl -nomodule -fpp -D__INTEL -D__FFTW > -D__USE_INTERNAL_FFTW -I../include -lfftw -I./ -I../Modules -I../ > iotk/src -I../PW -I../PH -I../CPV -c iotk_base.f90 > /hpc/mpich/bin/mpif90: line 332: eval: -O: invalid option > eval: usage: eval [arg ...] > > What does the above error mean? it means that your mpif90 script is broken > How to solve this problem? replace your mpif90 script with one that works Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From naivebamboo at hotmail.com Thu Dec 14 15:12:48 2006 From: naivebamboo at hotmail.com (naivebamboo Huang) Date: Thu, 14 Dec 2006 09:12:48 -0500 Subject: [Pw_forum] Specify the states to be pseudized In-Reply-To: <57B44F22-AEB5-4540-82CD-1002D4039B25@nest.sns.it> Message-ID: Thanks very much. This is what I chosed. But I saw it required 4 wave functions. Can I set the other two "label and occupancy" as "6d and 0.0", "6f and 0.0"? Another choice is "4f , 14" and "5d, 10"? I want to reproduce the pseudopotential from PHI code and this is why I attached the input file for PHI code. Both of the configurations can make the conversion successful. But when I check both configurations, there are some NaN in the output (energy). So I guess they are not appropriate. Please let me know if I am wrong. Thanks a lot Baoling Huang >From: Paolo Giannozzi >Reply-To: pw_forum at pwscf.org >To: pw_forum at pwscf.org >Subject: Re: [Pw_forum] Specify the states to be pseudized >Date: Thu, 14 Dec 2006 10:52:49 +0100 > > >On Dec 14, 2006, at 4:27 , naivebamboo Huang wrote: > >>I downloaded the PBE pseudopotential for Bi from abinit website >>and tried to convert it to UPF format. When I run fhi2upf.x, I was >>asked to input "label, occupancy" . I don't know how to do that >>because I know little about the details of pseudopotential. > >but you should know that the Bi atom has [Xe] 4f14 5d10 6s2 6p3 >electronic configuration, so the labels and occupancies of the valence >states are 6s and 2, 6p and 3, presumably > >>Another related question is how to specify the states to be pseudized >>in ld1.x > >it is explained in detail in the documentation (atomic_doc/) > >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 _________________________________________________________________ Get the latest Windows Live Messenger 8.1 Beta version.?Join now. http://ideas.live.com From giannozz at nest.sns.it Thu Dec 14 15:17:37 2006 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 14 Dec 2006 15:17:37 +0100 Subject: [Pw_forum] the error message which I can not recognized. In-Reply-To: <847567.73573.qm@web73001.mail.tp2.yahoo.com> References: <847567.73573.qm@web73001.mail.tp2.yahoo.com> Message-ID: <80820DBE-E36C-4BB0-BE04-B3FCBEBF4490@nest.sns.it> On Dec 14, 2006, at 14:51 , ? ?? wrote: > ** ON ENTRY TO ZHPEV PARAMETER NUMBER 1 HAD AN > ILLEGAL VALUE please look for ZHPEV in the mailling list archive and you will find this: http://www.democritos.it/pipermail/pw_forum/2004-December/001774.html Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From srijan.india at gmail.com Thu Dec 14 15:39:38 2006 From: srijan.india at gmail.com (Srijan Kumar Saha) Date: Thu, 14 Dec 2006 20:09:38 +0530 Subject: [Pw_forum] compilation error In-Reply-To: References: <3fcc7e670612120605r36efeb98pe0309b084cfa6957@mail.gmail.com> <3fcc7e670612140542v13b5e572s828731e844ae74db@mail.gmail.com> Message-ID: <3fcc7e670612140639n680e7dccq710632acc6c8faee@mail.gmail.com> Dear Sir, >>>>>>>>>mpif90 -O2 -tpp6 -assume byterecl -nomodule -fpp -D__INTEL -D__FFTW > > -D__USE_INTERNAL_FFTW -I../include -lfftw -I./ -I../Modules -I../ > > iotk/src -I../PW -I../PH -I../CPV -c iotk_base.f90 > > /hpc/mpich/bin/mpif90: line 332: eval: -O: invalid option > > eval: usage: eval [arg ...] > > > > What does the above error mean? > > it means that your mpif90 script is broken > > > How to solve this problem? > > >>>>>>>>>>>>replace your mpif90 script with one that works The script that works in my system is /hpc/mpich/bin/mpif90. I don't have the script /opt/mpich/intel/bin/mpif90 which works very well in my friend's system.. But I did not understand that in which file of esspresso, I have to replace the /hpc/mpich/bin/mpif90 script? With best regards, Srijan -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061214/570293f5/attachment.htm From prasenjit.jnc at gmail.com Thu Dec 14 16:14:37 2006 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Thu, 14 Dec 2006 16:14:37 +0100 Subject: [Pw_forum] compilation error In-Reply-To: <3fcc7e670612140639n680e7dccq710632acc6c8faee@mail.gmail.com> References: <3fcc7e670612120605r36efeb98pe0309b084cfa6957@mail.gmail.com> <3fcc7e670612140542v13b5e572s828731e844ae74db@mail.gmail.com> <3fcc7e670612140639n680e7dccq710632acc6c8faee@mail.gmail.com> Message-ID: <627e0ffa0612140714g62b0f559y23ec07e2fdb6eff8@mail.gmail.com> when u do ./configure, it should be identified. If not in the make.sys file, which is in the main directory ($espresso-ver). The flags which u need to change are:F90/MPIF90 and F77/MPIF77 Hope this helps. Prasenjit. On 12/14/06, Srijan Kumar Saha wrote: > > > > Dear Sir, > > >>>>>>>>>mpif90 -O2 -tpp6 -assume byterecl -nomodule -fpp -D__INTEL > > -D__FFTW > > > -D__USE_INTERNAL_FFTW -I../include -lfftw -I./ -I../Modules -I../ > > > iotk/src -I../PW -I../PH -I../CPV -c iotk_base.f90 > > > /hpc/mpich/bin/mpif90: line 332: eval: -O: invalid option > > > eval: usage: eval [arg ...] > > > > > > What does the above error mean? > > > > it means that your mpif90 script is broken > > > > > How to solve this problem? > > > > >>>>>>>>>>>>replace your mpif90 script with one that works > > > > > The script that works in my system is /hpc/mpich/bin/mpif90. > > I don't have the script /opt/mpich/intel/bin/mpif90 which works very > well > in my friend's system.. > > But I did not understand that in which file of esspresso, I have to > replace the /hpc/mpich/bin/mpif90 script? > > > With best regards, > Srijan > -- PRASENJIT GHOSH, Ph. D STUDENT, THEORETICAL SCIENCES UNIT, JNCASR, BANGALORE-560064, INDIA. PHONE: OFFICE : +91-80-22082835/34 MOBILE: +91-9880519401 -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061214/47dce1ae/attachment.htm From chen_shao_hua197 at yahoo.com.tw Thu Dec 14 16:53:53 2006 From: chen_shao_hua197 at yahoo.com.tw (=?big5?q?=B3=AF=20=A4=D6=B5=D8?=) Date: Thu, 14 Dec 2006 23:53:53 +0800 (CST) Subject: [Pw_forum] the error message which I can not recognized. In-Reply-To: <80820DBE-E36C-4BB0-BE04-B3FCBEBF4490@nest.sns.it> Message-ID: <148555.69950.qm@web73004.mail.tp2.yahoo.com> Thank you very much. max --- Paolo Giannozzi ?? > > On Dec 14, 2006, at 14:51 , ? ?? wrote: > > > ** ON ENTRY TO ZHPEV PARAMETER NUMBER 1 HAD AN > > ILLEGAL VALUE > > please look for ZHPEV in the mailling list archive > and you will find > this: > http://www.democritos.it/pipermail/pw_forum/2004-December/001774.html > > 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 > ___________________________________________________ ??????? ? ???????????????? http://messenger.yahoo.com.tw/ From giannozz at nest.sns.it Thu Dec 14 17:18:44 2006 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 14 Dec 2006 17:18:44 +0100 Subject: [Pw_forum] Specify the states to be pseudized In-Reply-To: References: Message-ID: <53D0BD8A-E144-48ED-A27B-34C6A32D252A@nest.sns.it> On Dec 14, 2006, at 15:12 , naivebamboo Huang wrote: > Thanks very much. This is what I chosed. But I saw it required > 4 wave functions. Can I set the other two "label and occupancy" > as "6d and 0.0", "6f and 0.0"? "5f and 0.0", I guess. The main quantum number is not used, anyway > Another choice is "4f , 14" and "5d, 10"? 29 valence electrons ? wow! Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From naivebamboo at hotmail.com Fri Dec 15 06:08:52 2006 From: naivebamboo at hotmail.com (naivebamboo Huang) Date: Fri, 15 Dec 2006 00:08:52 -0500 Subject: [Pw_forum] Specify the states to be pseudized In-Reply-To: <53D0BD8A-E144-48ED-A27B-34C6A32D252A@nest.sns.it> Message-ID: Dear Paolo, Thanks. I checked the ground state of Bi and thought the "label, occupancy" can be 6S 2 6P 3 7S 0 6D 0 Is the sequence of the input important? I mean, if I input "7S, 0" first in the conversion, is the result the same? (considering fhi may have some sequence) Also, I don't know if FHI input use the same "label, occupancy" (it only give the configuration [Xe] 4f14 5d10 6s2 6p3). These are not clear in the document about fhi2upf.x . Yes, 29 valence electron may be too many, does it cause problem except efficiency? (some of them are in core state in fact) Thanks Baoling >From: Paolo Giannozzi >Reply-To: pw_forum at pwscf.org >To: pw_forum at pwscf.org >Subject: Re: [Pw_forum] Specify the states to be pseudized >Date: Thu, 14 Dec 2006 17:18:44 +0100 > > >On Dec 14, 2006, at 15:12 , naivebamboo Huang wrote: > >>Thanks very much. This is what I chosed. But I saw it required >>4 wave functions. Can I set the other two "label and occupancy" >>as "6d and 0.0", "6f and 0.0"? > >"5f and 0.0", I guess. The main quantum number is not used, anyway > >>Another choice is "4f , 14" and "5d, 10"? > >29 valence electrons ? wow! > >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 _________________________________________________________________ Get free, personalized commercial-free online radio with MSN Radio powered by Pandora http://radio.msn.com/?icid=T002MSN03A07001 From giannozz at nest.sns.it Fri Dec 15 14:04:31 2006 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 15 Dec 2006 14:04:31 +0100 Subject: [Pw_forum] Specify the states to be pseudized In-Reply-To: References: Message-ID: <04717CA1-4688-4DA6-92A2-0931A7B2C398@nest.sns.it> On Dec 15, 2006, at 6:08 , naivebamboo Huang wrote: > Dear Paolo, > Thanks. I checked the ground state of Bi and thought the "label, > occupancy" can be > 6S 2 > 6P 3 > 7S 0 > 6D 0 no it cannot: conventional pseudopotentials have one potential per l, so if you have four potentials, they are s,p,d,f. > Is the sequence of the input important? I mean, if I input "7S, 0" > first in the conversion, is the result the same? (considering fhi > may have some sequence) Also, I don't know if FHI input use > the same "label, occupancy" (it only give the configuration > [Xe] 4f14 5d10 6s2 6p3). These are not clear in the document > about fhi2upf.x . labels are used only to label atomic pseudo-wavefunctions. Occupancies are used only to generate the starting charge. The only really important parameter in the conversion is lloc. Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From babazade at gmail.com Fri Dec 15 14:18:57 2006 From: babazade at gmail.com (Amin Babazadeh) Date: Fri, 15 Dec 2006 16:48:57 +0330 Subject: [Pw_forum] about epsilon In-Reply-To: <458147DD.8030700@sissa.it> References: <458147DD.8030700@sissa.it> Message-ID: Dear Degironc Thanks a lot for your recommendation but i don't know how to make pseudopotential my job is about finding optical properties of ZnS and ZnS nanostructure with using espresso. I will be so appreciate if you help me and find ZnS pseudopotential in your archive.I need your help. Thanks a lot On 12/14/06, degironc wrote: > > Dear Amin, > using US PP would be preferable but if this is not possible one > option is to use a Zn pseudopotential that bury the 3d orbital in the > core. You NEED THEN to use non-linear core correction in the > pseudopotential otherwise very poor results are obtained but with NLCC > some decent description comes out for semiconductors [see for instance > Ferroelectrics 111, 19 (1990); Phys. Rev. B 47, 3588 (1993), Phys. > Rev. Lett. 80, 4939 (1998), Appl. Phys. Lett. 75, 2746 (1999) ]. > Unfortunately I don't have at hand any of the Zn pseudopotentials > used in those works... I ll' try to dig in my archives but you may also > try to generate one using ld1.x code (maybe modifying the input for As > or the one for Al that are included in atomoc_doc/pseudo-gen/ ... ) > stefano > > Amin Babazadeh wrote: > > > Dear Andrea > > Thanks a lot for your clear answer. > > I have another question.do you have a any idea for solving my problem > > i will appreciate if you give me some idea. > > can i find pseudopotential from other cods like abinit?I didn't work > > with abinit or it's pseudopotentail but i see in the espresso's > > mailing list that some people use the abinit pseudopotentail. > > thanks a lot > > > > On 12/14/06, *Andrea Ferretti* > > wrote: > > > > > > > > > > > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > from epsilon : error # 1 > > > USPP are not implemented > > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > > > > > > > > i think this error says that the epsilon.x doesn't work on US > > > pseudopotential > > > > this is exactly the point, you are right... > > > > > ------ > > > IF ( okvan ) CALL errore('epsilon','USPP are not implemented',1) > > > ------ > > > i don't know what okvan is?is this mean a spatial kind of USPP i > > should use > > > or it said that i can't use US pseudopotential. > > > > okwan is a logical variable which is .TRUE. if at least one of the > > pseudopotentials in the calculation is ultrasoft (or vanderbilt > > type)... > > > > > > > I also want to test it with non conserving potential bur > > unfortunately i > > > couldn't find any pseudopotential for ZnS. > > > > unfortunately, while S does not need USPP, Zn is it quite hard in > > terms of > > cutoff energy, and therefore, after a brief check, it seems the > > pseudopage > > of espresso does not contain any norm-conserving pseudo for Zn. > > > > andrea > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > > > > -- > > AMIN > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- AMIN -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061215/9def66d9/attachment.htm From amit76.india at gmail.com Fri Dec 15 18:00:54 2006 From: amit76.india at gmail.com (Amit Kumar) Date: Fri, 15 Dec 2006 22:30:54 +0530 Subject: [Pw_forum] electron-phonon interaction ... Message-ID: Respected Users, *How to cope with the following error*? electron-phonon interaction ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from lint : error # 148 cannot remap grid on k-point list %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... Regards, Amit -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061215/8c33e99f/attachment.htm From srijan.india at gmail.com Fri Dec 15 19:01:52 2006 From: srijan.india at gmail.com (Srijan Kumar Saha) Date: Fri, 15 Dec 2006 23:31:52 +0530 Subject: [Pw_forum] Raman Active Mode Message-ID: <3fcc7e670612151001r2f04ab48i9713dde81bfd86c8@mail.gmail.com> Dear Pwscf Users, Using ph.x we can get all the Gamma point phonon frequencies for a particular system. In PWSCF, Is there any post processing executable which can identify only the Raman active phonons among all the obtained phonons? With best Regards, Srijan -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061215/5120d987/attachment.htm From proffess at yandex.ru Sat Dec 16 01:34:09 2006 From: proffess at yandex.ru (Sergey Lisenkov) Date: Sat, 16 Dec 2006 03:34:09 +0300 (MSK) Subject: [Pw_forum] C_POINTER on ibm power4 Message-ID: <45833F01.000005.03236@webmail9.yandex.ru> Dear users, In new version of pwscf (3.2) the parameter C_POINTER in include/fft_defs.h is defined by configure and can be integer*8 (64-bit case) and integer*4 (32-bit case), if I am not totally mistaken. On Power4+ architecture (with environment variable OBJECT_MODE=64, which enables 64-bit version) configure defines compilation option "-q64" in both FFLAGS and LDFLAGS. However, C_POINTER is defined as integer*4. I guessed that it was error and replaced it by integer*8. When my calculations started I saw in the output file: G cutoff = 316.5977 (******* G-vectors) FFT grid: (198,198,***) G cutoff = 9.0456 ( 93393 G-vectors) smooth grid: ( 36, 36,168) The system is not too big to have z component of FFT of "***". It should be around 392 (info from the another machine). So, does it mean that on IBM Power4 I have to redefine C_POINTER as integer*4 (as it was defined by configure)? Thanks, Sergey From babazade at gmail.com Sat Dec 16 09:28:49 2006 From: babazade at gmail.com (Amin Babazadeh) Date: Sat, 16 Dec 2006 11:58:49 +0330 Subject: [Pw_forum] compilation error In-Reply-To: <3fcc7e670612140542v13b5e572s828731e844ae74db@mail.gmail.com> References: <3fcc7e670612120605r36efeb98pe0309b084cfa6957@mail.gmail.com> <3fcc7e670612140542v13b5e572s828731e844ae74db@mail.gmail.com> Message-ID: Dear Srijan i told you what you should to do.it didn't work? if you compile the ifort you can do ./configure MPIF90=ifort and then make all i hope that you succeed in your job On 12/14/06, Srijan Kumar Saha wrote: > > > > > Respected Users, > > I have changed the previous ifort compiler. > Now I'm getting the following error. > > configure: success > > /espresso-3.2 > make all > test -d bin || mkdir bin > if test -d iotk ; then \ > ( cd iotk ; if test "make" = "" ; then make TLDEPS= libiotk.a ; \ > else make TLDEPS= libiotk.a ; fi ) ; fi > make[1]: Entering directory `/home/espresso-3.2/iotk' > cd src ; make libiotk.a > make[2]: Entering directory `/home/espresso-3.2/iotk/src' > mpif90 -O2 -tpp6 -assume byterecl -nomodule -fpp -D__INTEL -D__FFTW > -D__USE_INTERNAL_FFTW -I../include -lfftw -I./ -I../Modules -I../iotk/src > -I../PW -I../PH -I../CPV -c iotk_base.f90 > /hpc/mpich/bin/mpif90: line 332: eval: -O: invalid option > eval: usage: eval [arg ...] > make[2]: *** [iotk_base.o] Error 2 > make[2]: Leaving directory `/home/espresso-3.2/iotk/src' > make[1]: *** [libiotk.a] Error 2 > make[1]: Leaving directory `/home/espresso-3.2/iotk' > make: *** [libiotk] Error 2 > > What does the above error mean? > How to solve this problem? > > With best regards, > Srijan > -- AMIN -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061216/19ce561c/attachment.htm From wierzbom at ts.infn.it Sat Dec 16 11:49:39 2006 From: wierzbom at ts.infn.it (Malgorzata Wierzbowska) Date: Sat, 16 Dec 2006 11:49:39 +0100 (CET) Subject: [Pw_forum] electron-phonon interaction ... In-Reply-To: References: Message-ID: On Fri, 15 Dec 2006, Amit Kumar wrote: Dear Users, As for the answer to the question below and similar ones (e.g. when the error is followed by a message from the code) I can advice the first debugging/input_check step: -- goto the code and find sobroutine which gives the error or grep the error message in the source by making for instance grep -i "cannot remap grid on k-point list" ./*/*.f90 (or PH/*.f90) -- if you find that place, you may see "a hint" --------------- do n=1,nkh do nk=1,nkBZ if (eqBZ(nk) == n) go to 20 end do ! this failure of the algorithm may indicate that the displaced grid ! (with k1,k2,k3.ne.0) does not have the full symmetry of the lattice call errore('lint','cannot remap grid on k-point list',n) 20 continue end do ------------------------------- -- You think what are "k1,k2,k3" in the code. You find that you should specify these numbers as zero in the input (otherwise there are problems with the symmetry... because somebody -- read Gosia in this case -- was lazy to solve it). -- You change your input, and if it still doesn't work.... you send us your input. If you solve your little problems on your own you will feel satifaction! Have fun, Gosia > Respected Users, > > *How to cope with the following error*? > > electron-phonon interaction ... > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from lint : error # 148 > cannot remap grid on k-point list > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > > Regards, > Amit > From amit76.india at gmail.com Sat Dec 16 13:31:53 2006 From: amit76.india at gmail.com (Amit Kumar) Date: Sat, 16 Dec 2006 18:01:53 +0530 Subject: [Pw_forum] Electron-phonon interaction ... Message-ID: Respected Sir, I think the error is not so simple. Because I did all what you think a student is supposed to do before posting a problem. Here is my input ------> cat > hexagonal_2D_sample.scf.fit.in << EOF &control calculation='scf' restart_mode='from_scratch', prefix='hexa', pseudo_dir = '$PSEUDO_DIR/', outdir='$TMP_DIR/' tstress = .true. tprnfor = .true. / &system ibrav = 4, celldm(1) = 4.16, celldm(3) = 16.0, nat = 2, ntyp = 1, ecutwfc =40.0, ecutrho = 240.0, occupations='smearing', smearing='methfessel-paxton', degauss=0.01, la2F = .true., / &electrons conv_thr = 1.0d-8 mixing_beta = 0.7 ATOMIC_POSITIONS (angstrom) A 0.000000000 0.001189495 0.000000000 A 0.000000000 1.418810505 0.000000000 K_POINTS {automatic} 32 32 4 **************************************************************************** Same input file for SCF calculation only with out la2F flag and with K_POINTS {automatic} 8 8 1 ***************************************************************************** cat > hexagonal_2D_sample.elph.in << EOF Electron-phonon coefficients for 2D hexagoanl sample &inputph tr2_ph=1.0d-10, prefix='hexa', fildvscf='hexadv', amass(1)=58.9332, outdir='$TMP_DIR/', fildyn='hexa.dyn', elph=.true., trans=.true., ldisp=.true. nq1=4, nq2=4, nq3=1 / EOF $ECHO " running the el-ph calculation...\c" ******************************************************************************************************* I have checked for several combinations of K_POINTS and nq1, nq2 and nq3 also. But I' still getting the same error. Looking forward to your kind help. Regards, Amit As for the answer to the question below and similar ones (e.g. when the error is followed by a message from the code) I can advice the first debugging/input_check step: -- goto the code and find sobroutine which gives the error or grep the error message in the source by making for instance grep -i "cannot remap grid on k-point list" ./*/*.f90 (or PH/*.f 90) -- if you find that place, you may see "a hint" -- You think what are "k1,k2,k3" in the code. You find that you sh ould specify these numbers as zero in the input (otherwise there are problems with the symmetry... because somebody -- read Gosi a in this case -- was lazy to solve it). -- You change your input, and if it still doesn't work.... you sen d us your input.. -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061216/bd3c4c98/attachment.htm From akohlmey at cmm.chem.upenn.edu Sat Dec 16 14:44:22 2006 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sat, 16 Dec 2006 14:44:22 +0100 Subject: [Pw_forum] C_POINTER on ibm power4 In-Reply-To: <45833F01.000005.03236@webmail9.yandex.ru> References: <45833F01.000005.03236@webmail9.yandex.ru> Message-ID: <7b6913e90612160544m5182a56bsf1af5976b1f8788c@mail.gmail.com> On 12/16/06, Sergey Lisenkov wrote: > > Dear users, > > In new version of pwscf (3.2) the parameter C_POINTER in include/fft_defs.h > is defined by configure and can be integer*8 (64-bit case) and integer*4 > (32-bit case), if I am not totally mistaken. On Power4+ architecture (with > environment variable OBJECT_MODE=64, which enables 64-bit version) configure > defines compilation option "-q64" in both FFLAGS and LDFLAGS. However, > C_POINTER is defined as integer*4. I guessed that it was error and replaced > it by integer*8. When my calculations started I saw in the output file: > > G cutoff = 316.5977 (******* G-vectors) FFT grid: (198,198,***) > G cutoff = 9.0456 ( 93393 G-vectors) smooth grid: ( 36, 36,168) > > The system is not too big to have z component of FFT of "***". It should be > around 392 (info from the another machine). So, does it mean that on IBM > Power4 I have to redefine C_POINTER as integer*4 (as it was defined by dear sergey, if you have trouble with the size of pointers, you would get segmentation faults and NaNs but not '****' outputs. those seems actually possible, 198/36 is 5.5. 168*5.5 is 924. if 36 is much larger than the actually required xy-grid then you'd have a factor of ~6 which would give you a z-grid of > 1000. if you grep through the sources, you'll see that C_POINTER is used only to interface to the intel mkl and fftw. if you use neither, having C_POINTER defined to the wrong value should not affect you in case you are using essl. cheers, axel. > configure)? > > Thanks, > Sergey > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From wierzbom at ts.infn.it Sat Dec 16 17:52:50 2006 From: wierzbom at ts.infn.it (Malgorzata Wierzbowska) Date: Sat, 16 Dec 2006 17:52:50 +0100 (CET) Subject: [Pw_forum] Electron-phonon interaction ... In-Reply-To: References: Message-ID: First: I am not a "resected Sir" but a "simple female user" ;-) Second: if you followed my earlier advice you would find what to do.... I will tell you how: From words: ! this failure of the algorithm may indicate that the displaced grid ! (with k1,k2,k3.ne.0) does not have the full symmetry of the lattice one can guess that k1, k2, k3 are input parameters. Then one could look to files which read input, (by making: ls ./*/*inp*.f90). The answer is: ----------------------------------- ./CPV/input.f90 ./flib/linpack.f90 ./PH/bcast_ph_input.f90 ./D3/bcast_d3_input.f90 ./Modules/input_parameters.f90 ./PW/input.f90 ./flib/inpfile.f90 ./PH/bcast_ph_input1.f90 ./VIB/read_input_vib.f90 ------------------------------ Now we need to find these files which contain "k1" or "k2" or "k3" (by making: grep -i 'k2' ./*/*inp*.f90) The answer is: ------------------------- ............... ./PW/input.f90: k2_ = k2 ............... ------------------------------------ We look into PW/input.f90 and we see: ------------ IF ( k_points == 'automatic' ) THEN ! ! ... automatic generation of k-points ! gamma_only = .FALSE. lxkcry = .FALSE. nks = 0 ! ! ... nk1,nk2,nk3 and k1,k2,k3 are initialized even when not used ! nk1_ = nk1 nk2_ = nk2 nk3_ = nk3 k1_ = k1 k2_ = k2 k3_ = k3 ------------------------- Which means that for automatic k-points the k-point shift (k1,k2,k3) is not set by default to zero like it is done for other choices of the k-point coordinates. You should therefore put your k-points as follows: 32 32 4 0 0 0 and 8 8 1 0 0 0 I have checked that above works for hegagonal magnesium. Third: I can guess from your "cut_and_changed" input why do you want to do el-ph with spin. If you want to implement it you need to work a bit because it will not be so fast and easy work as you may think now. You may start from hexagonal Mg, which is nonmagnetic. Learn equations which are behind phonons and el-ph, for instance from Baroni S, de Gironcoli S, Dal Corso A, et al. Phonons and related crystal properties from density-functional perturbation theory REVIEWS OF MODERN PHYSICS 73 (2): 515-562 APR 2001 There is another publication closer to the implementation of elph with USPP: Dal Corso A Density-functional perturbation theory with ultrasoft pseudopotentials PHYSICAL REVIEW B 64 (23): Art. No. 235118 DEC 15 2001 After you think you understand above, you should write these equations with spin. At this point you should understand some "factors of 2" which might be in front of el-ph coefficients or in front of DOS in case of calculations without spin. Then go to the code and find matrixes and vectors you need. Then check how the simple scf is implemented with spin (I mean how spin is passed through the code) and combine above knowledge. Gosia On Sat, 16 Dec 2006, Amit Kumar wrote: > Respected Sir, > > I think the error is not so simple. > Because I did all what you think a student is supposed to > do before posting a problem. > > Here is my input ------> > > cat > hexagonal_2D_sample.scf.fit.in << EOF > &control > calculation='scf' > restart_mode='from_scratch', > prefix='hexa', > pseudo_dir = '$PSEUDO_DIR/', > outdir='$TMP_DIR/' > tstress = .true. > tprnfor = .true. > / > &system > ibrav = 4, > celldm(1) = 4.16, > celldm(3) = 16.0, > nat = 2, > ntyp = 1, > ecutwfc =40.0, > ecutrho = 240.0, > occupations='smearing', > smearing='methfessel-paxton', > degauss=0.01, > la2F = .true., > / > &electrons > conv_thr = 1.0d-8 > mixing_beta = 0.7 > > ATOMIC_POSITIONS (angstrom) > A 0.000000000 0.001189495 0.000000000 > A 0.000000000 1.418810505 0.000000000 > > K_POINTS {automatic} > 32 32 4 > > **************************************************************************** > Same input file for SCF calculation only with out la2F flag and > with > > K_POINTS {automatic} > 8 8 1 > ***************************************************************************** > cat > hexagonal_2D_sample.elph.in << EOF > Electron-phonon coefficients for 2D hexagoanl sample > &inputph > tr2_ph=1.0d-10, > prefix='hexa', > fildvscf='hexadv', > amass(1)=58.9332, > outdir='$TMP_DIR/', > fildyn='hexa.dyn', > elph=.true., > trans=.true., > ldisp=.true. > nq1=4, nq2=4, nq3=1 > / > EOF > $ECHO " running the el-ph calculation...\c" > > ******************************************************************************************************* > > I have checked for several combinations of K_POINTS and nq1, nq2 and nq3 > also. > But I' still getting the same error. > > Looking forward to your kind help. > > > Regards, > Amit > > > As for the answer to the question below and similar ones > (e.g. when the error is followed by a message from the code) > I can advice the first debugging/input_check step: > > -- goto the code and find sobroutine which gives the error > or grep the error message in the source by making for instance > grep -i "cannot remap grid on k-point list" ./*/*.f90 (or PH/*.f > 90) > -- if you find that place, you may see "a hint" > > -- You think what are "k1,k2,k3" in the code. You find that you sh > ould > specify these numbers as zero in the input (otherwise there > are problems with the symmetry... because somebody -- read Gosi > a > in this case -- was lazy to solve it). > -- You change your input, and if it still doesn't work.... you sen > d us > your input.. > From marzari at MIT.EDU Sat Dec 16 19:07:40 2006 From: marzari at MIT.EDU (Nicola Marzari) Date: Sat, 16 Dec 2006 13:07:40 -0500 Subject: [Pw_forum] scaling on clusters with different communication types In-Reply-To: References: Message-ID: <458435EC.60505@mit.edu> Dear Kader, we usually test cp, rather than pwscf, and have only used gigabit ethernet. Usually, our clusters are divided in nodes of 4 or 6 or 8 blades, where each blade is either a Pentium 4, a Dual Xeon, or a Core 2 Duo, and each node has its own private gigabit switch (i.e. the master node connects to all blades with a master switch, and each node of 4/6/8 blades has its own second independent gigabit switch). Intel processors work very well as single CPU performance, but saturate the memory bus very rapidly. For this reason, in our applications a dual Xeon is usually only 25% faster than a single Pentium, or a dual chip / quad core Woodcrest is only ~30% faster than a single chip / dual core at the same clock speed. One important statement: The quality of the gigabit switch and the quality of the gigabit controller on the motherboard have an enormous influence on the results. You can find in http://quasiamore.mit.edu/ESPRESSO/CP90_tests/ a summary of our standard test - bulk AgI in a cubic cell of 30x30x30 a.u. with 108 atoms, 20 Ry cutoff (160 Ry cutoff on the charge density), and 486 bands (i.e. 972 electrons). Note that the cp code has changed during the years, become slightly slower at first, and faster lately. If you read this, you might get an idea of what to expect - our key numbers are for how long it takes, in seconds, to do 5 CP steps on this system. The best performance that we get, at this stage, is 23.4s per CP step, on 6 Core 2 Duo: http://quasiamore.mit.edu/ESPRESSO/CP90_tests/CP90.timings.large Let me summarize the most important points: 1) the quality of the gigabit switches makes an important difference. None of the 6-7 currently available that we tested performed as well as a much older one we purchased 2 years ago. We tested expensive managed and unmanaged ones. No idea why this is. 2) the quality of the on-board ethernet controller is extremely important. Our dual xeon cluster, with Dell SC1425, scales much better (up to 8 blades) than our latest Core 2 Duo (with PDSMI+ motherboards, and specifically Intel 82573L/V ethernet controllers), that at most scales on 3 blades. This is on rerasonably comparable workload, and we cannot think at any other variable than the controller. 3) we have been experimenting with a new MPI protocol (MPI-GAMMA) from Giuseppe Ciaccio in Genova, and this seems to be working very well, with excellent scaling up to 6 Core 2 Duo blades. This is still experimental, and we plan to release more complete info in January. Thanks to Nicola Bonini, Arash Mostofi, and Young-Su Lee for all the careful tests listed above. nicola Kara, Abdelkader wrote: > Dear all, > > Greatings. > > I will appreciate it very much if you can share with me your experience > of running pwscf on clusters with different communication hardware. > I am interested in the scaling with the number of CPU's for the following 3 > different communication types: > 1)gigabit ethernet > 2) myrinet > 3) InfiniBand > > Thank you very much for your input on this matter > > Kader Kara > > Physics Department > University of Central Florida > _______________________________________________ > 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 naivebamboo at hotmail.com Sat Dec 16 23:31:10 2006 From: naivebamboo at hotmail.com (naivebamboo Huang) Date: Sat, 16 Dec 2006 17:31:10 -0500 Subject: [Pw_forum] Trouble in LD1.x Message-ID: Dear PWscf users, I am trying to construct the pseudopotential for Bi. The following is my input: &INPUT iswitch = 3 , atom = 'Bi' , config = '[Xe] 4f14 5d10 6s2 6p3' , rel = 1 , lsd = 0 , dft = 'PBE' , title = 'Bi' , prefix = 'allelectron' , latt = 0 , isic = 0 , nld = 4 , rlderiv = 2.5 , eminld = -4.0 , emaxld = 4.0 , deld = 0.02 , / &InputP pseudotype = 2 , file_pseudopw = '/home/huang/pwscf/work/Bi2Te3/Bi.pbe.UPF' , lloc = -1 , rcloc = 2.3 , tm = .true. , nlcc = .false. , lpaw = .false. , / 3 5D 3 2 10.000 0.000 2.10 2.40 6S 1 0 2.000 0.000 2.20 2.50 6P 2 1 3.000 0.000 2.30 2.50 &TEST nconf = 1 , / But there always appears an error: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_psconfig : error # 1 reading nwfs %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Could anyone help me? Is there any other problem in my input? Thanks very much Baoling Huang _________________________________________________________________ MSN Shopping has everything on your holiday list. Get expert picks by style, age, and price. Try it! http://shopping.msn.com/content/shp/?ctId=8000,ptnrid=176,ptnrdata=200601&tcode=wlmtagline From amit76.india at gmail.com Sun Dec 17 06:21:20 2006 From: amit76.india at gmail.com (Amit Kumar) Date: Sun, 17 Dec 2006 10:51:20 +0530 Subject: [Pw_forum] Electron-phonon interaction ... In-Reply-To: References: Message-ID: Dear Malgorzata, It's very nice to recieve your useful suggestions. I tried all the combinations---> 32 32 4 0 0 0, 32 32 32, 32 32 4 1 1 1 --->>> every possible combinations before posting this problem on the forum. But I got the same following error again and again. electron-phonon interaction ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from lint : error # 23 cannot remap grid on k-point list %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... I think the source of the above error is something different. My guess:::: The dense grid must contain all k and k+q grid points used in the e-p calculation. How do we know the above condition has been satisfied for automatic generated k and q points with nk1=32, nk2=32, nk3=4 and nq1=4, nq2=4, nq3=1?????? Here is my q-point grid:::: Calculation of the dynamical matrices for ( 4, 4, 1,) uniform grid of q-points ( 7q-points): N xq(1) xq(2) xq(3) 1 0.00000 0.00000 0.00000 2 0.00000 0.28868 0.00000 3 0.00000 -0.57735 0.00000 4 0.25000 0.14434 0.00000 5 0.25000 0.43301 0.00000 6 -0.50000 -0.28868 0.00000 7 -0.50000 0.00000 0.00000 And my k-points grid is here:::: number of k points= 166 gaussian broad. (ryd)= 0.0100 nga uss = 1 cart. coord. in units 2pi/a_0 k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.0 312500 k( 2) = ( 0.0000000 0.2886751 0.0000000), wk = 0.0 000000 k( 3) = ( 0.0000000 0.1443376 0.0000000), wk = 0.0 104167 k( 4) = ( 0.0000000 0.4330127 0.0000000), wk = 0.0 000000 * * * k( 166) = ( 0.2500000 0.8660254 0.0000000), wk = 0.0000000 See!!!! 0.28868 and 0.2886751 are not exactly equal. Is this the possible reason for the error like "cannot remap grid on k-point list"????? I'm not sure any other there might be any other. Please help me to find out the unknown reason of this well known error and give me some clue to get rid of this error. Thank you again for your very very useful letter. Regards, Amit > -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061217/92b2f20a/attachment.htm From proffess at yandex.ru Sun Dec 17 15:50:54 2006 From: proffess at yandex.ru (Sergey Lisenkov) Date: Sun, 17 Dec 2006 17:50:54 +0300 (MSK) Subject: [Pw_forum] C_POINTER on ibm power4 In-Reply-To: <7b6913e90612160544m5182a56bsf1af5976b1f8788c@mail.gmail.com> References: <45833F01.000005.03236@webmail9.yandex.ru> <7b6913e90612160544m5182a56bsf1af5976b1f8788c@mail.gmail.com> Message-ID: <4585594E.000003.01808@colgate.yandex.ru> dear axel, thanks for the help. Indeed I found the error - I put extra "0" in my ecutrho value (3500 instead 350). Now everything is OK. >if you grep through the sources, you'll see that C_POINTER is used >only to interface to the intel mkl and fftw. if you use neither, having >C_POINTER defined to the wrong value should not affect you in case >you are using essl. yes, I'm using essl. In case of C_POINTER integer*4 the code works too, as you mentioned. thanks, sergey From proffess at yandex.ru Sun Dec 17 16:33:14 2006 From: proffess at yandex.ru (Sergey Lisenkov) Date: Sun, 17 Dec 2006 18:33:14 +0300 (MSK) Subject: [Pw_forum] calculation crashes after reading charge density Message-ID: <4585633A.00000F.03421@webmail11.yandex.ru> dear all, I do have the following problem (it occurs only on ibm power4 machine, code is pw 3.2.0). I am performing the atomic relaxation and calculations stop (due to timelimit of queue) after several successful bfgs steps. I resume calculation using new atomic coordinates and put " startingpot='file' " in my input file. However, in this case the code crashed immediately : G cutoff = 31.6598 ( 697757 G-vectors) FFT grid: ( 64, 64,360) G cutoff = 9.0456 ( 106713 G-vectors) smooth grid: ( 36, 36,192) nbndx = 1532 nbnd = 383 natomwfc = 456 npwx = 829 nelec = 638.00 nkb = 888 ngl = 18256 The initial density is read from file : intf.save/charge-density.xml starting charge 640.36115, renormalised to 638.00000 negative rho (up, down): 0.900E-05 0.000E+00 Parameters of the lda+U calculation: Number of iteration with fixed ns = 0 Starting ns and Hubbard U : enter write_ns .... total cpu time spent up to now is 177.60 secs WARNING: integrated charge= 636.11804878, expected= 638.00000000 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from electrons : error # 1 charge is wrong %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... It does not happen on other machine (Xeon cluster) using the same input file. Any hints? thanks, sergey From wierzbom at ts.infn.it Sun Dec 17 16:41:51 2006 From: wierzbom at ts.infn.it (Malgorzata Wierzbowska) Date: Sun, 17 Dec 2006 16:41:51 +0100 (CET) Subject: [Pw_forum] Electron-phonon interaction ... In-Reply-To: References: Message-ID: On Sun, 17 Dec 2006, Amit Kumar wrote: In the k-points input we read a line with numbers nk1 nk2 nk3 k1 k2 k3 where (k1,k2,k3) is a shift-vector from the origin. For the el-ph calculation (and I guess also for the integration with the tetrahedra method) we need to specify k1=k2=k3=0 ---- So your "32 32 4 1 1 1" for sure is wrong. You need to take "32 32 4 0 0 0". You are right that all k and k+q have to belong to the dense grid. But see: All your meshes are in the same BZ and they are generated by division of the reciprocal lattice vectors b1,b2,b3 by numbers nk1, nk2, nk3 (above is true also for q-point grid nq1, nq2, nq3). To check whether your your k and k+q are in dense k-mesh, You need to see whether dense nk1 divided by rare nk1 gives integer and whether dense nk1 divided by nq1 gives integer. If above 2 conditions are satisfied, you check direction b2 and b3 in your cell: I mean dense_nk2/nq2 and dense_nk3/nq3 and dense_nk2/rare_nk2 etc. If all above give integers -- which is your case -- your error does not occur. -- So let us check your meshes: dense 32 32 4 0 0 0 rare 8 8 1 0 0 0 phonon 4 4 1 (it should be default here that they are not shifted) direction b1: 32/8=integer, 32/4=integer, also k+q is OK because 8/4=integer the same for b2 direction b3: 4/1=integer For me it works for hehagonal Mg. Please do my excercise I attach the script. Gosia > Dear Malgorzata, > > It's very nice to recieve your useful suggestions. > I tried all the combinations---> > 32 32 4 0 0 0, 32 32 32, > 32 32 4 1 1 1 --->>> every possible combinations before posting this > problem on the forum. > But I got the same following error again and again. > > electron-phonon interaction ... > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from lint : error # 23 > cannot remap grid on k-point list > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > > > I think the source of the above error is something different. > > My guess:::: > > The dense grid must contain all k and k+q grid points used in the > e-p calculation. > > How do we know the above condition has been satisfied for automatic > generated k and q points with nk1=32, nk2=32, nk3=4 and > nq1=4, nq2=4, nq3=1?????? > > Here is my q-point grid:::: > > Calculation of the dynamical matrices for ( 4, 4, 1,) uniform grid of > q-points > ( 7q-points): > N xq(1) xq(2) xq(3) > 1 0.00000 0.00000 0.00000 > 2 0.00000 0.28868 0.00000 > 3 0.00000 -0.57735 0.00000 > 4 0.25000 0.14434 0.00000 > 5 0.25000 0.43301 0.00000 > 6 -0.50000 -0.28868 0.00000 > 7 -0.50000 0.00000 0.00000 > > And my k-points grid is here:::: > > number of k points= 166 gaussian broad. (ryd)= 0.0100 nga > uss = 1 > cart. coord. in units 2pi/a_0 > k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.0 > 312500 > k( 2) = ( 0.0000000 0.2886751 0.0000000), wk = 0.0 > 000000 > k( 3) = ( 0.0000000 0.1443376 0.0000000), wk = 0.0 > 104167 > k( 4) = ( 0.0000000 0.4330127 0.0000000), wk = 0.0 > 000000 > > * > * > * k( 166) = ( 0.2500000 0.8660254 0.0000000), wk = 0.0000000 > > See!!!! 0.28868 and 0.2886751 are not exactly equal. > > Is this the possible reason for the error like > "cannot remap grid on k-point list"????? > > I'm not sure any other there might be any other. > Please help me to find out the unknown reason of this well known > error and give me some clue to get rid of this error. > > Thank you again for your very very useful letter. > > Regards, > Amit > > > >> > -------------- next part -------------- # # SCF at dense k-mesh, good enough for electronic DOS # cat > mg.scf.fit.in << EOF &control calculation='scf' restart_mode='from_scratch', prefix='mg', pseudo_dir = '$PSEUDO_DIR/', outdir='$TMP_DIR/' / &system ibrav= 4, celldm(1) = 6.06, celldm(3)= 3.21, nat= 2, ntyp= 1, ecutwfc =15.0, occupations='smearing', smearing='methfessel-paxton', degauss=0.01, la2F = .true., / &electrons conv_thr = 1.0d-8 mixing_beta = 0.7 / ATOMIC_SPECIES Mg 24.3 Mg.pz-n-vbc.UPF ATOMIC_POSITIONS {crystal} Mg 0.333333333 0.666666666 0.25 Mg 0.666666666 0.333333333 0.75 K_POINTS {automatic} 32 32 4 0 0 0 EOF $ECHO " running the scf calculation with dense k-point grid...\c" $PW_COMMAND < mg.scf.fit.in > mg.scf.fit.out $ECHO " done" # # SCF at k-mesh good enough for phonons # cat > mg.scf.in << EOF &control calculation='scf' restart_mode='from_scratch', prefix='mg', pseudo_dir = '$PSEUDO_DIR/', outdir='$TMP_DIR/' / &system ibrav= 4, celldm(1) = 6.06, celldm(3)= 3.21, nat= 2, ntyp= 1, ecutwfc =15.0, occupations='smearing', smearing='methfessel-paxton', degauss=0.01, / &electrons conv_thr = 1.0d-8 mixing_beta = 0.7 / ATOMIC_SPECIES Mg 24.3 Mg.pz-n-vbc.UPF ATOMIC_POSITIONS {crystal} Mg 0.333333333 0.666666666 0.25 Mg 0.666666666 0.333333333 0.75 K_POINTS {automatic} 8 8 1 0 0 0 EOF $ECHO " running the scf calculation...\c" $PW_COMMAND < mg.scf.in > mg.scf.out $ECHO " done" # cat > mg.elph.in << EOF Electron-phonon coefficients for Mg &inputph tr2_ph=1.0d-10, prefix='mg', fildvscf='mgdv', amass(1)=24.3, outdir='$TMP_DIR/', fildyn='mg.dyn', elph=.true., trans=.true., ldisp=.true. nq1=4, nq2=4, nq3=1 / EOF $ECHO " running the el-ph calculation...\c" $PH_COMMAND < mg.elph.in > mg.elph.out $ECHO " done" # # q2r and matdyn # cat > q2r.in << EOF &input zasr='simple', fildyn='mg.dyn', flfrc='Mg444.fc', la2F=.true. / EOF $ECHO " running q2r...\c" $Q2R_COMMAND < q2r.in > q2r.out $ECHO " done" # # # cat > matdyn.in.freq << EOF &input asr='simple', amass(1)=26.98, flfrc='Mg444.fc', flfrq='Mg444.freq', la2F=.true., dos=.false. / 19 0.000 0.0 0.0 0.0 0.125 0.0 0.0 0.0 0.250 0.0 0.0 0.0 0.375 0.0 0.0 0.0 0.500 0.0 0.0 0.0 0.750 0.0 0.0 0.0 1.000 0.0 0.0 0.0 0.825 0.125 0.125 0.0 0.750 0.250 0.250 0.0 0.625 0.375 0.375 0.0 0.500 0.500 0.500 0.0 0.325 0.325 0.325 0.0 0.250 0.250 0.250 0.0 0.125 0.125 0.125 0.0 0.000 0.000 0.000 0.0 0.125 0.125 0.000 0.0 0.250 0.250 0.000 0.0 0.325 0.325 0.000 0.0 0.500 0.500 0.000 0.0 EOF $ECHO " running matdyn for frequency calculation...\c" $MATDYN_COMMAND < matdyn.in.freq > matdyn.out.freq $ECHO " done" # # # cat > matdyn.in.dos << EOF &input asr='simple', amass(1)=26.98, flfrc='Mg444.fc', flfrq='Mg444.freq', la2F=.true., dos=.true. fldos='phonon.dos', nk1=10, nk2=10, nk3=10, ndos=50 / EOF $ECHO " running matdyn for a2F(omega) calculation...\c" $MATDYN_COMMAND < matdyn.in.dos > matdyn.out.dos $ECHO " done" From jhashemifar at gmail.com Mon Dec 18 12:23:28 2006 From: jhashemifar at gmail.com (Javad hashemifar) Date: Mon, 18 Dec 2006 12:23:28 +0100 Subject: [Pw_forum] ambiguity in stress calculation Message-ID: <2fb18d9f0612180323o35680587r45df63f7cd620c99@mail.gmail.com> Dear Pwscf users Concerning the "tstress" input variable in the namelist 'control', I found the following explanation in the prepared sample INPUT_PW file: tstress LOGICAL calculate stress. Set to .TRUE. if calculation='vc-md' Does it mean that the calculated stress for other type of calculations (such as 'scf' and 'relax') is meaningless and is incorrect. I mean if we set tstress=.TRUE. in calculations='relax' then obtained stress values are correct or not. Thanks in advance for your answers Javad Hashemifar On 12/17/06, Malgorzata Wierzbowska wrote: > On Sun, 17 Dec 2006, Amit Kumar wrote: > > > In the k-points input we read a line with numbers > nk1 nk2 nk3 k1 k2 k3 > where (k1,k2,k3) is a shift-vector from the origin. > For the el-ph calculation (and I guess also for the integration > with the tetrahedra method) we need to specify k1=k2=k3=0 > > ---- So your "32 32 4 1 1 1" for sure is wrong. > You need to take "32 32 4 0 0 0". > > You are right that all k and k+q have to belong to the dense grid. > But see: All your meshes are in the same BZ and they are generated > by division of the reciprocal lattice vectors b1,b2,b3 by numbers > nk1, nk2, nk3 (above is true also for q-point grid nq1, nq2, nq3). > > To check whether your your k and k+q are in dense k-mesh, > You need to see whether dense nk1 divided by rare nk1 gives integer > and whether dense nk1 divided by nq1 gives integer. > If above 2 conditions are satisfied, you check direction b2 and b3 > in your cell: I mean dense_nk2/nq2 and dense_nk3/nq3 > and dense_nk2/rare_nk2 etc. If all above give integers -- > which is your case -- your error does not occur. > > -- So let us check your meshes: > dense 32 32 4 0 0 0 > rare 8 8 1 0 0 0 > phonon 4 4 1 (it should be default here that they are not shifted) > > direction b1: 32/8=integer, 32/4=integer, also k+q is OK because 8/4=integer > the same for b2 > direction b3: 4/1=integer > > For me it works for hehagonal Mg. Please do my excercise I attach the script. > > Gosia > > > > > > Dear Malgorzata, > > > > It's very nice to recieve your useful suggestions. > > I tried all the combinations---> > > 32 32 4 0 0 0, 32 32 32, > > 32 32 4 1 1 1 --->>> every possible combinations before posting this > > problem on the forum. > > But I got the same following error again and again. > > > > electron-phonon interaction ... > > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > from lint : error # 23 > > cannot remap grid on k-point list > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > stopping ... > > > > > > I think the source of the above error is something different. > > > > My guess:::: > > > > The dense grid must contain all k and k+q grid points used in the > > e-p calculation. > > > > How do we know the above condition has been satisfied for automatic > > generated k and q points with nk1=32, nk2=32, nk3=4 and > > nq1=4, nq2=4, nq3=1?????? > > > > Here is my q-point grid:::: > > > > Calculation of the dynamical matrices for ( 4, 4, 1,) uniform grid of > > q-points > > ( 7q-points): > > N xq(1) xq(2) xq(3) > > 1 0.00000 0.00000 0.00000 > > 2 0.00000 0.28868 0.00000 > > 3 0.00000 -0.57735 0.00000 > > 4 0.25000 0.14434 0.00000 > > 5 0.25000 0.43301 0.00000 > > 6 -0.50000 -0.28868 0.00000 > > 7 -0.50000 0.00000 0.00000 > > > > And my k-points grid is here:::: > > > > number of k points= 166 gaussian broad. (ryd)= 0.0100 nga > > uss = 1 > > cart. coord. in units 2pi/a_0 > > k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.0 > > 312500 > > k( 2) = ( 0.0000000 0.2886751 0.0000000), wk = 0.0 > > 000000 > > k( 3) = ( 0.0000000 0.1443376 0.0000000), wk = 0.0 > > 104167 > > k( 4) = ( 0.0000000 0.4330127 0.0000000), wk = 0.0 > > 000000 > > > > * > > * > > * k( 166) = ( 0.2500000 0.8660254 0.0000000), wk = 0.0000000 > > > > See!!!! 0.28868 and 0.2886751 are not exactly equal. > > > > Is this the possible reason for the error like > > "cannot remap grid on k-point list"????? > > > > I'm not sure any other there might be any other. > > Please help me to find out the unknown reason of this well known > > error and give me some clue to get rid of this error. > > > > Thank you again for your very very useful letter. > > > > Regards, > > Amit > > > > > > > >> > > > > -- ====================================== Seyed Javad Hashemifar, Ph.D. [current:] Tel:+49-203-3794743 Fax:+49-203-3794742 Fachbereich Physik (AG Kratzer), Universitat Duisburg-Essen 47048 Dusiburg, Germany [permanent:] Tel: +98-311-3912375 Fax: +98-311-3912376 Physics Department, Isfahan University of Technology 84156 Isfahan, Iran --------------------------------------------------------------------------- From degironc at sissa.it Mon Dec 18 12:52:32 2006 From: degironc at sissa.it (degironc) Date: Mon, 18 Dec 2006 12:52:32 +0100 Subject: [Pw_forum] ambiguity in stress calculation In-Reply-To: <2fb18d9f0612180323o35680587r45df63f7cd620c99@mail.gmail.com> References: <2fb18d9f0612180323o35680587r45df63f7cd620c99@mail.gmail.com> Message-ID: <45868100.2010600@sissa.it> I means that stress calculation is mandatory when moving the cell and therefore it is set true. But you can ask the calculation of stress tensor also if you are not changing the cell (and it should be right). stefano Javad hashemifar wrote: > Dear Pwscf users > > Concerning the "tstress" input variable in the namelist 'control', I > found the following explanation in the prepared sample INPUT_PW file: > > tstress LOGICAL > calculate stress. Set to .TRUE. if calculation='vc-md' > > Does it mean that the calculated stress for other type of calculations > (such as 'scf' and 'relax') is meaningless and is incorrect. I mean i > we set tstress=.TRUE. in calculations='relax' then obtained stress > values are correct or not. > > Thanks in advance for your answers > Javad Hashemifar > From giannozz at nest.sns.it Mon Dec 18 12:53:05 2006 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 18 Dec 2006 12:53:05 +0100 Subject: [Pw_forum] ambiguity in stress calculation In-Reply-To: <2fb18d9f0612180323o35680587r45df63f7cd620c99@mail.gmail.com> References: <2fb18d9f0612180323o35680587r45df63f7cd620c99@mail.gmail.com> Message-ID: On Dec 18, 2006, at 12:23 , Javad hashemifar wrote: > tstress LOGICAL > calculate stress. Set to .TRUE. if calculation='vc-md' > > Does it mean that the calculated stress for other type of calculations > (such as 'scf' and 'relax') is meaningless and is incorrect. no: it means that it is set to true if you do a variable-cell simulation, regardless of its value. You can use this options in other cases as well (provided you calculate the self-consistent charge, of course) --- Paolo Giannozzi, Democritos and University of Udine, Italy From amit76.india at gmail.com Mon Dec 18 14:34:18 2006 From: amit76.india at gmail.com (Amit Kumar) Date: Mon, 18 Dec 2006 19:04:18 +0530 Subject: [Pw_forum] Electron-phonon interaction ... In-Reply-To: References: Message-ID: Dear Malgorzata, It' s very nice to recieve your amiable reply. I told you that the error was due to some other reason not due to k-point grid I have used. Yes!!!!!!!!!! I have found out the reason. It's due to celldm(3) (= 16.0 ) I have used. If I use small celldm(3) like you, then I'm also not getting any error. But I'm little confused. To study 2D case properly, we should use a large c/a ratio. Right????????? Then why a big ratio showing some different error like "can't remap k-point grid". Thank you very much for your kind help. Regards, Amit -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061218/a58ad27c/attachment.htm From giannozz at nest.sns.it Mon Dec 18 14:49:41 2006 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 18 Dec 2006 14:49:41 +0100 Subject: [Pw_forum] Trouble in LD1.x In-Reply-To: References: Message-ID: On Dec 16, 2006, at 23:31 , naivebamboo Huang wrote: > &TEST > nconf = 1 , > / > But there always appears an error: > > from read_psconfig : error # 1 > reading nwfs if you specify a 'test' configuration (which you do not need, except in some special case, for pseudopotential generation) you have to specify which one Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at nest.sns.it Mon Dec 18 14:55:01 2006 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 18 Dec 2006 14:55:01 +0100 Subject: [Pw_forum] Raman Active Mode In-Reply-To: <3fcc7e670612151001r2f04ab48i9713dde81bfd86c8@mail.gmail.com> References: <3fcc7e670612151001r2f04ab48i9713dde81bfd86c8@mail.gmail.com> Message-ID: <682AC808-DBB7-465A-BF2E-A86EBD9F0B84@nest.sns.it> On Dec 15, 2006, at 19:01 , Srijan Kumar Saha wrote: > In PWSCF, Is there any post processing executable which > can identify only the Raman active phonons among all the > obtained phonons? the last version of the phonon code prints (very tentative) symmetry labels, from which one might be able to distinguish Raman-active mdes Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From srijan.india at gmail.com Mon Dec 18 15:35:50 2006 From: srijan.india at gmail.com (Srijan Kumar Saha) Date: Mon, 18 Dec 2006 20:05:50 +0530 Subject: [Pw_forum] Raman Active Mode In-Reply-To: <682AC808-DBB7-465A-BF2E-A86EBD9F0B84@nest.sns.it> References: <3fcc7e670612151001r2f04ab48i9713dde81bfd86c8@mail.gmail.com> <682AC808-DBB7-465A-BF2E-A86EBD9F0B84@nest.sns.it> Message-ID: <3fcc7e670612180635n1b0eb717pa5cabd1a635bd436@mail.gmail.com> Dear Sir, Thank you for your reply. >>>>>>>>>the last version of the phonon code prints (very tentative) > symmetry labels, from which one might be able to distinguish > Raman-active mdes. Could you please give me some references or examples where I can get more informations about the identifying of Raman-active modes using pwscf. With best regards, Srijan -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061218/a46b0323/attachment.htm From jin.zhang.pku at gmail.com Mon Dec 18 15:50:24 2006 From: jin.zhang.pku at gmail.com (Jin Zhang) Date: Mon, 18 Dec 2006 22:50:24 +0800 Subject: [Pw_forum] Raman Active Mode In-Reply-To: <3fcc7e670612180635n1b0eb717pa5cabd1a635bd436@mail.gmail.com> References: <3fcc7e670612151001r2f04ab48i9713dde81bfd86c8@mail.gmail.com> <682AC808-DBB7-465A-BF2E-A86EBD9F0B84@nest.sns.it> <3fcc7e670612180635n1b0eb717pa5cabd1a635bd436@mail.gmail.com> Message-ID: <5d233b6a0612180650k2b3d00fbubac4a9a311d683c1@mail.gmail.com> Dear Saha, I think you probably want to get some standard textbooks about quantum chemistry which talk about Raman modes in a lot details. Regards, Jin Zhang On 12/18/06, Srijan Kumar Saha wrote: > > > > Dear Sir, > > > > > Thank you for your reply. > > > > > > >>>>>>>>>the last version of the phonon code prints (very tentative) > > symmetry labels, > > from which one might be able to distinguish > > Raman-active mdes. > > > Could you please give me some references or examples where I can get > more informations > about the identifying of Raman-active modes using pwscf. > > With best regards, > Srijan > > > > -- Dep. of Physics, Peking University Beijing, P.R.China Phone: 86-10-62-753-190 -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061218/0ae8b30d/attachment.htm From nguyenhalvt at yahoo.com Mon Dec 18 17:16:39 2006 From: nguyenhalvt at yahoo.com (Nguyen Ngoc Ha) Date: Mon, 18 Dec 2006 08:16:39 -0800 (PST) Subject: [Pw_forum] How to understand filplot output file? Message-ID: <446414.3945.qm@web31009.mail.mud.yahoo.com> Dear PWscf Users! I calculated Local Density of State at E_Fermi for CO, (not for plot). I received a filplot ouput file, but I can't understand what in this file (I'm sorry). Here is input: &INPUTPP outdir= '/home/hthp/Desktop/TMP/TMP2/' , filplot = LDOS_Ef , plot_num = 3, / &PLOT nfile = 0 , / Here is output: 36 36 72 36 36 72 2 2 14 10.486 1.000 2.1556 0.000 0.000 0.0000 278.547393 4.000 25.000 3 1 O 6.00 2 C 4.00 1 0.501441847 0.724188345 0.633062794 2 2 0.503410729 0.635483111 0.818920961 1 1.50E-26 3.67E-27 -1.46E-26 -1.83E-27 1.19E-26 5.43E-27 2.02E-27 -6.94E-27 -7.88E-27 1.05E-28 ... Please help me this problem. Best Regards! Nguyen, Ngoc Ha Hanoi University of Education Faculty of Chemistry Department of Physical Chemistry Tel: Office: 04/8330842 Home: 04/7681083 Mobile: 0912129517 __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From akohlmey at cmm.chem.upenn.edu Mon Dec 18 17:29:27 2006 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Mon, 18 Dec 2006 17:29:27 +0100 Subject: [Pw_forum] How to understand filplot output file? In-Reply-To: <446414.3945.qm@web31009.mail.mud.yahoo.com> References: <446414.3945.qm@web31009.mail.mud.yahoo.com> Message-ID: <7b6913e90612180829k4c24a1ccjf6222b156cee722@mail.gmail.com> On 12/18/06, Nguyen Ngoc Ha wrote: > Dear PWscf Users! > I calculated Local Density of State at E_Fermi for CO, > (not for plot). I received a filplot ouput file, but I > can't understand what in this file (I'm sorry). it is a temporary file with an 'internal' format. please check with the documentation (Doc/INPUT_PP): ! The two steps can be performed independently. In order to perform ! only step 2), leave namelist &inputpp blank. In order to perform ! only step 1), do not specify namelist &plot ! ! Intermediate results from step 1 can be saved to disk (see ! (variable "filplot" in &inputpp) and later read in step 2. ! Since the file with intermediate results is formatted, it ! can be safely transferred to a different machine. This ! also allows plotting of a linear combination (for instance, ! charge differences) by saving two intermediate files and ! combining them (see variables "weight" and "filepp" in &plot) if you need even more details about the contents of this file, you have to read the sourcecode. there have been plenty suggestions of how to locate the corresponding file for a specific feature posted here recently, so i'll skip that. note, that the format of intermediate files may be changed between different versions of the code (in order to accomodate new features). cheers, axel. > > Here is input: > &INPUTPP > outdir= > '/home/hthp/Desktop/TMP/TMP2/' , > filplot = LDOS_Ef , > plot_num = 3, > / > &PLOT > nfile = 0 , > / > > Here is output: > 36 36 72 36 36 72 2 2 > 14 10.486 1.000 2.1556 0.000 0.000 0.0000 > 278.547393 4.000 25.000 3 > 1 O 6.00 > 2 C 4.00 > 1 0.501441847 0.724188345 0.633062794 2 > 2 0.503410729 0.635483111 0.818920961 1 > 1.50E-26 3.67E-27 -1.46E-26 -1.83E-27 1.19E-26 > 5.43E-27 2.02E-27 -6.94E-27 -7.88E-27 1.05E-28 > ... > > Please help me this problem. > Best Regards! > > > Nguyen, Ngoc Ha > Hanoi University of Education > Faculty of Chemistry > Department of Physical Chemistry > Tel: Office: 04/8330842 > Home: 04/7681083 > Mobile: 0912129517 > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ======================================================================= 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 emenendez at macul.ciencias.uchile.cl Mon Dec 18 20:04:34 2006 From: emenendez at macul.ciencias.uchile.cl (Eduardo Ariel Menendez P) Date: Mon, 18 Dec 2006 16:04:34 -0300 (CLST) Subject: [Pw_forum] Trouble in LD1.x In-Reply-To: <20061218173001.31183.68465.Mailman@democritos.sissa.it> References: <20061218173001.31183.68465.Mailman@democritos.sissa.it> Message-ID: Hi, I have a pseudopotential for Bi, pbe functional, troulliers-martins type, not warranted at all. Generating pseudos is my less favorite task with ESPRESSO, but it is working reasonably. I remember someone (Axel Kohlmeyer?) sent me other pseudo, when I asked for it in the forum. I offer mine to put in the web site. Eduardo > > On Dec 16, 2006, at 23:31 , naivebamboo Huang wrote: > > > &TEST > > nconf = 1 , > > / > > > But there always appears an error: > > > > from read_psconfig : error # 1 > > reading nwfs > > if you specify a 'test' configuration (which you do not need, > except in some special case, for pseudopotential generation) > you have to specify which one > > From babazade at gmail.com Tue Dec 19 07:32:24 2006 From: babazade at gmail.com (Amin Babazadeh) Date: Tue, 19 Dec 2006 10:02:24 +0330 Subject: [Pw_forum] Zn pseudopotential Message-ID: Dear users I am looking for Zn pseudopotential which hasn't been made by USPP.would you please tell me where can i find it. I will appreciate if anybody give it to me. Sincerely yours -- AMIN -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061219/fbfad0f2/attachment.htm From amit76.india at gmail.com Tue Dec 19 08:16:45 2006 From: amit76.india at gmail.com (Amit Kumar) Date: Tue, 19 Dec 2006 12:46:45 +0530 Subject: [Pw_forum] Electron-phonon interaction ... In-Reply-To: References: Message-ID: > Dear Malgorzata, I have not recieved your reply yet. Have you checked your sample Mg-script??? It's working fine for your celldm(3) = 3.21 but giving the error even for celldm(3) = 4.21. I'm confused. I think it's not expected. Right???? Waiting for your suggestions. Regards, Amit It' s very nice to recieve your amiable reply. > I told you that the error was due to some other reason not due to > k-point grid I have used. > Yes!!!!!!!!!! I have found out the reason. > It's due to celldm(3) (= 16.0 ) I have used. > If I use small celldm(3) like you, then I'm also not getting any error. > > But I'm little confused. To study 2D case properly, we should use a > large c/a ratio. > Right????????? Then why a big ratio showing some different error like > "can't remap k-point grid". > Thank you very much for your kind help. > > Regards, > Amit > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061219/6792043d/attachment.htm From ding at sissa.it Tue Dec 19 08:16:20 2006 From: ding at sissa.it (Xunlei Ding) Date: Tue, 19 Dec 2006 08:16:20 +0100 Subject: [Pw_forum] Zn pseudopotential In-Reply-To: References: Message-ID: <458791C4.3070303@sissa.it> Dear Amin, Here you can find some: http://www.pwscf.org/pseudo/1.3/html/Zn.html Yours sincerely, Ding Amin Babazadeh wrote: > Dear users > I am looking for Zn pseudopotential which hasn't been made by > USPP.would you please tell me where can i find it. > I will appreciate if anybody give it to me. > Sincerely yours > > -- > AMIN From babazade at gmail.com Tue Dec 19 10:08:04 2006 From: babazade at gmail.com (Amin Babazadeh) Date: Tue, 19 Dec 2006 12:38:04 +0330 Subject: [Pw_forum] Zn pseudopotential In-Reply-To: <458791C4.3070303@sissa.it> References: <458791C4.3070303@sissa.it> Message-ID: dear Xunlei i know there are some pseudopotential in Pwscf web site but for Zn all of them have been made by USPP i need some other pseudopotential that has been made for example by NCPP. Sincerely yours amin On 12/19/06, Xunlei Ding wrote: > > Dear Amin, > Here you can find some: > http://www.pwscf.org/pseudo/1.3/html/Zn.html > > Yours sincerely, > Ding > > Amin Babazadeh wrote: > > > Dear users > > I am looking for Zn pseudopotential which hasn't been made by > > USPP.would you please tell me where can i find it. > > I will appreciate if anybody give it to me. > > Sincerely yours > > > > -- > > AMIN > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- AMIN -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061219/4f9cc033/attachment.htm From lanhaiping at gmail.com Tue Dec 19 10:10:49 2006 From: lanhaiping at gmail.com (lan haiping) Date: Tue, 19 Dec 2006 17:10:49 +0800 Subject: [Pw_forum] Zn pseudopotential In-Reply-To: References: <458791C4.3070303@sissa.it> Message-ID: Hi, Amin, you can try to find NCPP from Martin's Web or from abinit .. regards, hai-ping On 12/19/06, Amin Babazadeh wrote: > > dear Xunlei > i know there are some pseudopotential in Pwscf web site but for Zn all of > them have been made by USPP i need some other pseudopotential that has been > made for example by NCPP. > Sincerely yours > amin > > On 12/19/06, Xunlei Ding wrote: > > > > Dear Amin, > > Here you can find some: > > http://www.pwscf.org/pseudo/1.3/html/Zn.html > > > > Yours sincerely, > > Ding > > > > Amin Babazadeh wrote: > > > > > Dear users > > > I am looking for Zn pseudopotential which hasn't been made by > > > USPP.would you please tell me where can i find it. > > > I will appreciate if anybody give it to me. > > > Sincerely yours > > > > > > -- > > > AMIN > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > AMIN -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061219/23bf634c/attachment.htm From wierzbom at ts.infn.it Tue Dec 19 11:15:55 2006 From: wierzbom at ts.infn.it (Malgorzata Wierzbowska) Date: Tue, 19 Dec 2006 11:15:55 +0100 (CET) Subject: [Pw_forum] Zn pseudopotential In-Reply-To: References: <458791C4.3070303@sissa.it> Message-ID: On Tue, 19 Dec 2006, Amin Babazadeh wrote: For the generation of Zn PP you can use espresso/atomic/ld1.x. There is an example of the input below. Be ware: necessary energy cutoff will be high if you include d-shell. =============================================== &input atom='Zn', config='[Ar] 3d10.0 4s2.0 4p0.0 ', dft='pz' rlderiv=3.0, eminld=-3.0, emaxld= 1.0 nld=3 iswitch=3 / &inputp pseudotype=1, lloc=0, file_pseudopw='Zn.mt' rho0=0.01 / 3 4P 2 1 0.00 0.00 2.50 2.50 3D 3 2 10.00 0.00 1.20 1.20 4S 1 0 2.00 0.00 2.20 2.20 &test ecutmin=100.0, ecutmax=200.0, decut=20.0 / 3 4P 2 1 0.00 0.00 2.50 2.50 3D 3 2 10.00 0.00 1.20 1.20 4S 1 0 2.00 0.00 2.20 2.20 ================================================== Gosia > dear Xunlei > i know there are some pseudopotential in Pwscf web site but for Zn all of > them have been made by USPP i need some other pseudopotential that has been > made for example by NCPP. > Sincerely yours > amin > > On 12/19/06, Xunlei Ding wrote: >> >> Dear Amin, >> Here you can find some: >> http://www.pwscf.org/pseudo/1.3/html/Zn.html >> >> Yours sincerely, >> Ding >> >> Amin Babazadeh wrote: >> >> > Dear users >> > I am looking for Zn pseudopotential which hasn't been made by >> > USPP.would you please tell me where can i find it. >> > I will appreciate if anybody give it to me. >> > Sincerely yours >> > >> > -- >> > AMIN >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > From wierzbom at ts.infn.it Tue Dec 19 11:19:10 2006 From: wierzbom at ts.infn.it (Malgorzata Wierzbowska) Date: Tue, 19 Dec 2006 11:19:10 +0100 (CET) Subject: [Pw_forum] Electron-phonon interaction ... In-Reply-To: References: Message-ID: On Tue, 19 Dec 2006, Amit Kumar wrote: >> Dear Malgorzata, > I have not recieved your reply yet. Because yesterday afternoon I was doing something else and soon I will go home for Christmas. But I will look to your problem before. > Have you checked your sample Mg-script??? > It's working fine for your celldm(3) = 3.21 but giving the error > even for celldm(3) = 4.21. I'm confused. I think it's not > expected. Right???? I will look. > > Waiting for your suggestions. > I will send you soon. > Regards, > Amit > Gosia > > It' s very nice to recieve your amiable reply. >> I told you that the error was due to some other reason not due to >> k-point grid I have used. >> Yes!!!!!!!!!! I have found out the reason. >> It's due to celldm(3) (= 16.0 ) I have used. >> If I use small celldm(3) like you, then I'm also not getting any error. >> >> But I'm little confused. To study 2D case properly, we should use a >> large c/a ratio. >> Right????????? Then why a big ratio showing some different error like >> "can't remap k-point grid". >> Thank you very much for your kind help. >> >> Regards, >> Amit >> >> >> > From ezadshojaee at hotmail.com Tue Dec 19 12:24:18 2006 From: ezadshojaee at hotmail.com (Ezad Shojaee) Date: Tue, 19 Dec 2006 11:24:18 +0000 Subject: [Pw_forum] eigenvectors in phonon calculation Message-ID: hi i am trying to calculate phonon frequencies by a grid for my case & i want to know that how should i know the eigenvector related to a special mode ( frequency ) for example the forth mode at gamma point ( to know that what is the vibration like in this mode ) thanx in advance _________________________________________________________________ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ From yuwen_66 at yahoo.com Tue Dec 19 12:30:01 2006 From: yuwen_66 at yahoo.com (W. YU) Date: Tue, 19 Dec 2006 03:30:01 -0800 (PST) Subject: [Pw_forum] phonon calculaiton- shifted k points or not? Message-ID: <751176.91418.qm@web51010.mail.yahoo.com> Thanks to Stefano, Paolo and all other pw users. Now I hope to make sure about something on phonon and e-ph coupling calculations. Stefano has told me a lot about consistancy while choosing parameters for scf and nonscf. But I still have two questions here. First for phonon calculation: it seems we can use both shifted and unshifted k points for scf and nscf(phonon), but unshifted q points for phonon. The q point grid is not necessarily a factor of k point grid. I reached the above conclusions from example06 for AlAs where the scf and nscf calculations using shifted k points which comes from a 222 grid, and the q points from a unshifted 444 grid. Second, for e-ph coupling. it seems we must use all unshifted k points and the from the readme of example07, the dense grid must contain all k and k+q grid points used in subsequent e-ph calculation. This is different from a pure phonon calculation. Please let know whether I am right or not! Thanks, Wen YU __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From ding at sissa.it Tue Dec 19 12:46:31 2006 From: ding at sissa.it (Xunlei Ding) Date: Tue, 19 Dec 2006 12:46:31 +0100 Subject: [Pw_forum] eigenvectors in phonon calculation In-Reply-To: References: Message-ID: <4587D117.1080104@sissa.it> Please try dynmat.x . Ezad Shojaee wrote: > hi > i am trying to calculate phonon frequencies by a grid for my case & i > want to know that how should i know the eigenvector related to a > special mode ( frequency ) for example the forth mode at gamma point > ( to know that what is the vibration like in this mode ) > thanx in advance > > _________________________________________________________________ > Express yourself instantly with MSN Messenger! Download today it's > FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From wierzbom at ts.infn.it Tue Dec 19 13:42:31 2006 From: wierzbom at ts.infn.it (Malgorzata Wierzbowska) Date: Tue, 19 Dec 2006 13:42:31 +0100 (CET) Subject: [Pw_forum] Electron-phonon interaction ... In-Reply-To: References: Message-ID: On Tue, 19 Dec 2006, Amit Kumar wrote: >> Dear Malgorzata, > > > I have not recieved your reply yet. > Have you checked your sample Mg-script??? > It's working fine for your celldm(3) = 3.21 but giving the error > even for celldm(3) = 4.21. I'm confused. I think it's not > expected. Right???? > I have checked that it is working with celldm(3) = 8.12 which is 5*1.624 (1.624 is c/a ratio in Mg hexagonal). > Waiting for your suggestions. > You need to change atomic positions in z-direction if you change c/a (if "normally", with c/a=1.624 you have 0.25 and 0.75, then for celldm(3)=5*hex, if you want 2 layer slab in the middle of the cell, you put 0.25 --> 0.5-0.25/5=0.45 and 0.75 --> 0.5+0.25/5=0.55 Here are mine: &system ibrav= 4, celldm(1) = 6.06, celldm(3)= 8.12, .............. ATOMIC_SPECIES Mg 24.3 Mg.pz-n-vbc.UPF ATOMIC_POSITIONS {crystal} Mg 0.333333333 0.666666666 0.45 Mg 0.666666666 0.333333333 0.55 K_POINTS.................................... There is no error! Gosia > Regards, > Amit > > > It' s very nice to recieve your amiable reply. >> I told you that the error was due to some other reason not due to >> k-point grid I have used. >> Yes!!!!!!!!!! I have found out the reason. >> It's due to celldm(3) (= 16.0 ) I have used. >> If I use small celldm(3) like you, then I'm also not getting any error. >> >> But I'm little confused. To study 2D case properly, we should use a >> large c/a ratio. >> Right????????? Then why a big ratio showing some different error like >> "can't remap k-point grid". >> Thank you very much for your kind help. >> >> Regards, >> Amit >> >> >> > From giannozz at nest.sns.it Tue Dec 19 15:31:54 2006 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 19 Dec 2006 15:31:54 +0100 Subject: [Pw_forum] calculation crashes after reading charge density In-Reply-To: <4585633A.00000F.03421@webmail11.yandex.ru> References: <4585633A.00000F.03421@webmail11.yandex.ru> Message-ID: <0E47D86C-C16E-4F14-8112-1CEBDDA006DC@nest.sns.it> On Dec 17, 2006, at 16:33 , Sergey Lisenkov wrote: > I do have the following problem (it occurs only on ibm power4 > machine, code is pw 3.2.0). I am performing the atomic relaxation > and calculations stop (due to timelimit of queue) after several > successful bfgs steps. I resume calculation using new atomic > coordinates and put " startingpot='file' " in my input file. and restart='restart' ? I am not sure you are supposed to do this > However, in this case the code crashed immediately it is very hard to find what is wrong in such a case, unless this behavior can be reproduced > The initial density is read from file : > intf.save/charge-density.xml > > starting charge 640.36115, renormalised to 638.00000 this is very strange: it means that the charge written to file was not correctly normalized, or that it was not correctly read Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From proffess at yandex.ru Tue Dec 19 15:43:57 2006 From: proffess at yandex.ru (Sergey Lisenkov) Date: Tue, 19 Dec 2006 17:43:57 +0300 (MSK) Subject: [Pw_forum] calculation crashes after reading charge density In-Reply-To: <0E47D86C-C16E-4F14-8112-1CEBDDA006DC@nest.sns.it> References: <4585633A.00000F.03421@webmail11.yandex.ru> <0E47D86C-C16E-4F14-8112-1CEBDDA006DC@nest.sns.it> Message-ID: <4587FAAD.000004.25184@soapbox.yandex.ru> dear Paolo, >and restart='restart' ? I am not sure you are supposed to do this NO, I don't use that. Only rho/pot is read. >this is very strange: it means that the charge written to file >was not correctly normalized, or that it was not correctly >read yes, it is very strange. For example, on another cluster using the same 3.2 version and almost the same example, I don't see this behavior: .... G cutoff = 31.6598 ( 785121 G-vectors) FFT grid: ( 64, 64,400) G cutoff = 9.0456 ( 119881 G-vectors) smooth grid: ( 36, 36,216) nbndx = 1768 nbnd = 442 natomwfc = 524 npwx = 1897 nelec = 736.00 nkb = 1008 ngl = 31261 The initial density is read from file : inif.save/charge-density.xml Parameters of the lda+U calculation: Number of iteration with fixed ns = 0 Starting ns and Hubbard U : enter write_ns U( 1) = 0.0000 U( 2) = 3.8710 U( 3) = 3.8710 U( 4) = 0.0000 U( 5) = 0.0000 U( 6) = 0.0000 .... nsum = 38.9538025 exit write_ns Atomic wfc used for LDA+U Projector are NOT orthogonalized Starting wfc are atomic total cpu time spent up to now is 86.21 secs Self-consistent Calculation iteration # 1 ecut= 25.00 Ry beta=0.20 .... I am not sure is it worth to send this job - it is a huge one (80 atoms, 5x5x30 A cell). Thanks, Sergey From giannozz at nest.sns.it Tue Dec 19 16:07:08 2006 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 19 Dec 2006 16:07:08 +0100 Subject: [Pw_forum] phonon calculaiton- shifted k points or not? In-Reply-To: <751176.91418.qm@web51010.mail.yahoo.com> References: <751176.91418.qm@web51010.mail.yahoo.com> Message-ID: <4EA3954F-E0B6-4942-937A-543C6A0875C8@nest.sns.it> On Dec 19, 2006, at 12:30 , W. YU wrote: > First for phonon calculation: it seems we can use both > shifted and unshifted k points for scf and nscf(phonon), > but unshifted q points for phonon. The q point grid is not > necessarily a factor of k point grid. you mean: "the choice of the q-point grid (i.e. the grid used to calculate the interatomic force constants) does not depend upon the k-point grid (i.e. the grid used to perform the self-consistent calculation")? Correct: the former depends upon the range of interatomic force constants in real space, the latter upon the character of the band structure > Second, for e-ph coupling. it seems we must use all > unshifted k points and the from the readme of > example07, the dense grid must contain all k and k+q > grid points used in subsequent e-ph calculation. I am not sure that the grid used in the scf calculation must be unshifted. What is sure is that the "dense grid" must contain all k-points used in the scf calculation and all the k+q points, where q are the phonon wavevector at which the electron-phonon coefficients are calculated Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From wenyu at sas.ustb.edu.cn Wed Dec 20 05:15:18 2006 From: wenyu at sas.ustb.edu.cn (WY) Date: Wed, 20 Dec 2006 12:15:18 +0800 Subject: [Pw_forum] phonon calculaiton- shifted k points or not? Message-ID: <366587563.29855@ustb.edu.cn> Dear Paolo, thank you for your answer! >you mean: "the choice of the q-point grid (i.e. the grid used >to calculate the interatomic force constants) does not depend >upon the k-point grid (i.e. the grid used to perform the >self-consistent calculation")? Exactly! >Correct: the former depends >upon the range of interatomic force constants in real space, >the latter upon the character of the band structure Doesn't the above answer agree with what I said in the former post? >I am not sure that the grid used in the scf calculation >must be unshifted. What is sure is that the "dense grid" >must contain all k-points used in the scf calculation and >all the k+q points, where q are the phonon wavevector >at which the electron-phonon coefficients are calculated The problem is: if you choose a shifted k-grid and a unshited q-grid, it seems difficult to maintain the above restrictions-namely the "the "dense grid" must contain all k-points used in the scf calculation and all the k+q points, where q are the phonon wavevector at which the electron-phonon coefficients are calculated" Best, Wen YU -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061220/bdfa1d92/attachment.htm From wenyu at sas.ustb.edu.cn Wed Dec 20 05:21:19 2006 From: wenyu at sas.ustb.edu.cn (WY) Date: Wed, 20 Dec 2006 12:21:19 +0800 Subject: [Pw_forum] phonon calculaiton- shifted k points or not? Message-ID: <366587925.03265@ustb.edu.cn> Dear Paolo, thank you for your answer! >you mean: "the choice of the q-point grid (i.e. the grid used >to calculate the interatomic force constants) does not depend >upon the k-point grid (i.e. the grid used to perform the >self-consistent calculation")? Exactly! >Correct: the former depends >upon the range of interatomic force constants in real space, >the latter upon the character of the band structure Doesn't the above answer agree with what I said in the former post? >I am not sure that the grid used in the scf calculation >must be unshifted. What is sure is that the "dense grid" >must contain all k-points used in the scf calculation and >all the k+q points, where q are the phonon wavevector >at which the electron-phonon coefficients are calculated The problem is: if you choose a shifted k-grid and a unshited q-grid, it seems difficult to maintain the above restrictions-namely the "the "dense grid" must contain all k-points used in the scf calculation and all the k+q points, where q are the phonon wavevector at which the electron-phonon coefficients are calculated" Best, Wen YU From srijan.india at gmail.com Wed Dec 20 07:09:13 2006 From: srijan.india at gmail.com (Srijan Kumar Saha) Date: Wed, 20 Dec 2006 11:39:13 +0530 Subject: [Pw_forum] Raman Active Mode In-Reply-To: <5d233b6a0612180650k2b3d00fbubac4a9a311d683c1@mail.gmail.com> References: <3fcc7e670612151001r2f04ab48i9713dde81bfd86c8@mail.gmail.com> <682AC808-DBB7-465A-BF2E-A86EBD9F0B84@nest.sns.it> <3fcc7e670612180635n1b0eb717pa5cabd1a635bd436@mail.gmail.com> <5d233b6a0612180650k2b3d00fbubac4a9a311d683c1@mail.gmail.com> Message-ID: <3fcc7e670612192209v17f1bc58ie0932cb1c4760d48@mail.gmail.com> Dear all, No, infact I want to get some more informations about pwscf package. Prof. Paolo wrote ::: the last version of the phonon code prints (very tentative) symmetry labels, from which one might be able to distinguish Raman-active modes So my confusions were ---> 1. the last version of the phonon code prints symmetry labels ---- When ???? For that should I use some special flag like IRAMAN = .true. or like that????? 2. (very tentative) ??? What does it mean????? Why very tentative???? 3. from which one might be able to distinguish Raman-active modes ??? Why might be????? Won't the output file give enough informations to identify Raman-active modes???? We know that the derivative of the *electronic* *polarizability *tensor with respect to a normal coordinate gives us the information about Raman -active modes. So does pwscf calculate the derivative of the *electronic* *polarizability *tensor??? I know my questions are very trivial to veterans. I'm just a *newbie in PWSCF. * So to clear my above confusions I just asked for some useful references or examples, not the answers of my trivial confusions. With best regards, Srijan On 12/18/06, Jin Zhang wrote: > > Dear Saha, > > I think you probably want to get some standard textbooks about quantum > chemistry which talk about Raman modes in a lot details. > > Regards, > Jin Zhang > > -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061220/ba17b97d/attachment.htm From babazade at gmail.com Wed Dec 20 14:55:29 2006 From: babazade at gmail.com (Amin Babazadeh) Date: Wed, 20 Dec 2006 17:25:29 +0330 Subject: [Pw_forum] Zn pseudopotential In-Reply-To: References: <458791C4.3070303@sissa.it> Message-ID: Dear Dr.Malgorzata Thanks a lot for your help.i put what you write me in a file and i run espresso-2.1.3/atomic/ld1.x but this error happened. from ld1_readin : error # 17 reading input namelist %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... I know that my question is simple but i hadn't made pseudopotential until i saw your mail.for solving problem i looked at the ld1_readin.f90 but there are many parameters in it that i don't know which one is necessary to write in the input file. would you please help me and tell me what i should add your written file?i wrote exactly &input atom='Zn', config='[Ar] 3d10.0 4s2.0 4p0.0 ', dft='pz' rlderiv=3.0, eminld=-3.0, emaxld= 1.0 nld=3 iswitch=3 / &inputp pseudotype=1, lloc=0, file_pseudopw='Zn.mt' rho0=0.01 / 3 4P 2 1 0.00 0.00 2.50 2.50 3D 3 2 10.00 0.00 1.20 1.20 4S 1 0 2.00 0.00 2.20 2.20 &test ecutmin=100.0, ecutmax=200.0, decut=20.0 / 3 4P 2 1 0.00 0.00 2.50 2.50 3D 3 2 10.00 0.00 1.20 1.20 4S 1 0 2.00 0.00 2.20 2.20 thanks a lot for your help sincerely yours amin On 12/19/06, Malgorzata Wierzbowska wrote: > > On Tue, 19 Dec 2006, Amin Babazadeh wrote: > > > For the generation of Zn PP you can use espresso/atomic/ld1.x. > There is an example of the input below. > Be ware: necessary energy cutoff will be high if you include d-shell. > > =============================================== > &input > atom='Zn', > config='[Ar] 3d10.0 4s2.0 4p0.0 ', > dft='pz' > rlderiv=3.0, > eminld=-3.0, > emaxld= 1.0 > nld=3 > iswitch=3 > / > &inputp > pseudotype=1, > lloc=0, > file_pseudopw='Zn.mt' > rho0=0.01 > / > 3 > 4P 2 1 0.00 0.00 2.50 2.50 > 3D 3 2 10.00 0.00 1.20 1.20 > 4S 1 0 2.00 0.00 2.20 2.20 > &test > ecutmin=100.0, ecutmax=200.0, decut=20.0 > / > 3 > 4P 2 1 0.00 0.00 2.50 2.50 > 3D 3 2 10.00 0.00 1.20 1.20 > 4S 1 0 2.00 0.00 2.20 2.20 > ================================================== > > Gosia > > > > > dear Xunlei > > i know there are some pseudopotential in Pwscf web site but for Zn all > of > > them have been made by USPP i need some other pseudopotential that has > been > > made for example by NCPP. > > Sincerely yours > > amin > > > > On 12/19/06, Xunlei Ding wrote: > >> > >> Dear Amin, > >> Here you can find some: > >> http://www.pwscf.org/pseudo/1.3/html/Zn.html > >> > >> Yours sincerely, > >> Ding > >> > >> Amin Babazadeh wrote: > >> > >> > Dear users > >> > I am looking for Zn pseudopotential which hasn't been made by > >> > USPP.would you please tell me where can i find it. > >> > I will appreciate if anybody give it to me. > >> > Sincerely yours > >> > > >> > -- > >> > AMIN > >> > >> _______________________________________________ > >> 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 > -- AMIN -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061220/58e763fe/attachment.htm From wierzbom at ts.infn.it Wed Dec 20 15:15:56 2006 From: wierzbom at ts.infn.it (Malgorzata Wierzbowska) Date: Wed, 20 Dec 2006 15:15:56 +0100 (CET) Subject: [Pw_forum] Zn pseudopotential In-Reply-To: References: <458791C4.3070303@sissa.it> Message-ID: On Wed, 20 Dec 2006, Amin Babazadeh wrote: I can't reproduce your error. I run exactly the same. Maybe there is some mistype in the input which I don't see.... How do you run it? Do you have this input in "file.in" and you run: "ld1.x < file.in" ? Maybe in the way you run the code ld1 does not see the input data.... ... just a guess..... Gosia > Dear Dr.Malgorzata > Thanks a lot for your help.i put what you write me in a file and i run > espresso-2.1.3/atomic/ld1.x > but this error happened. > > from ld1_readin : error # 17 > reading input namelist > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > stopping ... > I know that my question is simple but i hadn't made pseudopotential until i > saw your mail.for solving problem i looked at the ld1_readin.f90 but there > are many parameters in it that i don't know which one is necessary to write > in the input file. > would you please help me and tell me what i should add your written file?i > wrote exactly > &input > atom='Zn', > config='[Ar] 3d10.0 4s2.0 4p0.0 ', > dft='pz' > rlderiv=3.0, > eminld=-3.0, > emaxld= 1.0 > nld=3 > iswitch=3 > / > &inputp > pseudotype=1, > lloc=0, > file_pseudopw='Zn.mt' > rho0=0.01 > / > 3 > 4P 2 1 0.00 0.00 2.50 2.50 > 3D 3 2 10.00 0.00 1.20 1.20 > 4S 1 0 2.00 0.00 2.20 2.20 > &test > ecutmin=100.0, ecutmax=200.0, decut=20.0 > / > 3 > 4P 2 1 0.00 0.00 2.50 2.50 > 3D 3 2 10.00 0.00 1.20 1.20 > 4S 1 0 2.00 0.00 2.20 2.20 > > thanks a lot for your help > sincerely yours > amin > > > On 12/19/06, Malgorzata Wierzbowska wrote: >> >> On Tue, 19 Dec 2006, Amin Babazadeh wrote: >> >> >> For the generation of Zn PP you can use espresso/atomic/ld1.x. >> There is an example of the input below. >> Be ware: necessary energy cutoff will be high if you include d-shell. >> >> =============================================== >> &input >> atom='Zn', >> config='[Ar] 3d10.0 4s2.0 4p0.0 ', >> dft='pz' >> rlderiv=3.0, >> eminld=-3.0, >> emaxld= 1.0 >> nld=3 >> iswitch=3 >> / >> &inputp >> pseudotype=1, >> lloc=0, >> file_pseudopw='Zn.mt' >> rho0=0.01 >> / >> 3 >> 4P 2 1 0.00 0.00 2.50 2.50 >> 3D 3 2 10.00 0.00 1.20 1.20 >> 4S 1 0 2.00 0.00 2.20 2.20 >> &test >> ecutmin=100.0, ecutmax=200.0, decut=20.0 >> / >> 3 >> 4P 2 1 0.00 0.00 2.50 2.50 >> 3D 3 2 10.00 0.00 1.20 1.20 >> 4S 1 0 2.00 0.00 2.20 2.20 >> ================================================== >> >> Gosia >> >> >> >> > dear Xunlei >> > i know there are some pseudopotential in Pwscf web site but for Zn all >> of >> > them have been made by USPP i need some other pseudopotential that has >> been >> > made for example by NCPP. >> > Sincerely yours >> > amin >> > >> > On 12/19/06, Xunlei Ding wrote: >> >> >> >> Dear Amin, >> >> Here you can find some: >> >> http://www.pwscf.org/pseudo/1.3/html/Zn.html >> >> >> >> Yours sincerely, >> >> Ding >> >> >> >> Amin Babazadeh wrote: >> >> >> >> > Dear users >> >> > I am looking for Zn pseudopotential which hasn't been made by >> >> > USPP.would you please tell me where can i find it. >> >> > I will appreciate if anybody give it to me. >> >> > Sincerely yours >> >> > >> >> > -- >> >> > AMIN >> >> >> >> _______________________________________________ >> >> 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 >> > > > > From giannozz at nest.sns.it Wed Dec 20 15:20:18 2006 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 20 Dec 2006 15:20:18 +0100 Subject: [Pw_forum] Zn pseudopotential In-Reply-To: References: <458791C4.3070303@sissa.it> Message-ID: <764737FA-5265-46B8-9596-2539A0FC995F@nest.sns.it> On Dec 20, 2006, at 14:55 , Amin Babazadeh wrote: > i put what you write me in a file and i run espresso-2.1.3/atomic/ > ld1.x > but this error happened. > > from ld1_readin : error # 17 > reading input namelist 2.1.3 ? the input format of ld1.x has meanwhile changed Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From emenendez at macul.ciencias.uchile.cl Wed Dec 20 17:54:16 2006 From: emenendez at macul.ciencias.uchile.cl (Eduardo Ariel Menendez P) Date: Wed, 20 Dec 2006 13:54:16 -0300 (CLST) Subject: [Pw_forum] problem with control of temperature in pw Message-ID: Hello, I have some problems to do molecular dynamics using pw.x at a defined temperature (version 3.2 and 3.1.1). Please, take a look at the example04. To introduce a starting temperature I added tempw=300.D0 in si.md8.in. Following the documentation, this should set 300 K as starting T. However, the starting temperature remains 0 K. Moreover, using ion_temperature='rescaling', tempw=300.D0, nraise=1, (to rescale at each step) delta_t=1, it starts at 300 K. However, it is not evident that it rescales, unless it reports all the magnitudes just before rescaling. cat si.md8.out |grep 'kinetic energy (Ekin) =' kinetic energy (Ekin) = 0.01971053 Ry kinetic energy (Ekin) = 0.01951557 Ry kinetic energy (Ekin) = 0.01958081 Ry kinetic energy (Ekin) = 0.01967049 Ry ... cat si.md8.out |grep 'Ekin + Etot (const) = ' Ekin + Etot (const) = -62.15607665 Ry Ekin + Etot (const) = -62.15583900 Ry Ekin + Etot (const) = -62.15540873 Ry Ekin + Etot (const) = -62.15504154 Ry cat si.md8.out |grep temperat Starting temperature = 300.00 K temperature = 296.38506727 K temperature = 293.45347455 K temperature = 294.43450387 K temperature = 295.78296164 K Maybe this is because the magnitudes are reported just before rescaling. I see that reducing dt the fluctuations are reduced. Is is the case? Regards Eduardo From babazade at gmail.com Thu Dec 21 10:02:22 2006 From: babazade at gmail.com (Amin Babazadeh) Date: Thu, 21 Dec 2006 12:32:22 +0330 Subject: [Pw_forum] Zn pseudopotential In-Reply-To: <764737FA-5265-46B8-9596-2539A0FC995F@nest.sns.it> References: <458791C4.3070303@sissa.it> <764737FA-5265-46B8-9596-2539A0FC995F@nest.sns.it> Message-ID: Dear Dr.Molgorzata and Paolo The problem was that i have used the old version of espresso.Thank you for your helps. best the regards Amin On 12/20/06, Paolo Giannozzi wrote: > > > On Dec 20, 2006, at 14:55 , Amin Babazadeh wrote: > > > i put what you write me in a file and i run espresso-2.1.3/atomic/ > > ld1.x > > but this error happened. > > > > from ld1_readin : error # 17 > > reading input namelist > > 2.1.3 ? the input format of ld1.x has meanwhile changed > > 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 > -- AMIN -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061221/ffa65f51/attachment.htm From jhashemifar at gmail.com Fri Dec 22 09:20:21 2006 From: jhashemifar at gmail.com (Javad hashemifar) Date: Fri, 22 Dec 2006 09:20:21 +0100 Subject: [Pw_forum] problem in relaxation by using bfgs Message-ID: <2fb18d9f0612220020x36188117g36a386607ebfb157@mail.gmail.com> Dear Pwscf users I am trying to relax a tetragonal interface supercell at different values of vertical lattice parameter (celldm(3)). I am using calculation=relax and the namelist IONS is as follows: ion_dynamic = bfgs bfgs_ndim = 3, pot_extrapolation = "second_order", wfc_extrapolation = "second_order", I have done this relaxation at several values of celldm(3) to find the ones that has minimum energy and zero stress. Let me to note that I can use of vc-relax calculations for this purpose because celldm(1) is fixed. For some values of celldm(3) every thing is OK and the system relax well and both etot_conv_thr and forc_conv_thr satisfies. But in some other values of celldm(3) the calculation stops with the following error: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from checkallsym : error # 1 some of the original symmetry operations not satisfied %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% After more accurate consideration of the cases that have above error, I found that in that cases, the relaxation procedure has been done correctly for a few steps (2 - 3 step) and then in the last steps the position of atoms in x and y directions also has changed while there is no force in these two direction. But after that program has tried to symmetrize the position and change back the value of x and y positions as follows: ATOMIC_POSITIONS (alat) Ga 0.000000000 0.000000000 0.000000000 As 0.000000000 0.502872976 0.354710310 Cr 0.502872976 0.502872976 0.686421612 As 0.502872976 0.000000000 1.018132914 SYMMETRIZED ATOMIC COORDINATES) ATOMIC_POSITIONS (alat) Ga 0.000000000 0.000000000 0.000000000 As 0.000000000 0.500000000 0.350788698 Cr 0.500000000 0.500000000 0.682500000 As 0.500000000 0.000000000 1.014211302 and then the above mentioned error occurs. It is the situation for all the cases that relaxation has not been completed. When I restarted one of this cases with damp method (instead of bfgs) the above error did not appear and the system relaxed correctly. I would appreciate if some body explains why by using bfgs such errors occurs and how I can solve that. Otherwise I should use the damp method for relaxation that usually needs to more steps to reach to the minimum energy. thanks in advance Javad Hashemifar From hqzhou at nju.edu.cn Fri Dec 22 10:59:37 2006 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Fri, 22 Dec 2006 17:59:37 +0800 Subject: [Pw_forum] problem in relaxation by using bfgs References: <2fb18d9f0612220020x36188117g36a386607ebfb157@mail.gmail.com> Message-ID: <00c101c725af$e481ba00$1d00a8c0@solarflare> Javad, I got the same problem several months before. In my case, I noticed that if I run my job on equal to or less than 2 processors (or CPU cores), it will be OK. Another way to get rid of it is to comment out the pot and wfc extrapolation. Of course, this will slow down your calculation to some extent. I didn't try to use 'first_order', you may test this first. Huiqun ----- Original Message ----- From: "Javad hashemifar" To: Sent: Friday, December 22, 2006 4:20 PM Subject: [Pw_forum] problem in relaxation by using bfgs > Dear Pwscf users > > I am trying to relax a tetragonal interface supercell at different > values of vertical lattice parameter (celldm(3)). I am using > calculation=relax and the namelist IONS is as follows: > > ion_dynamic = bfgs > bfgs_ndim = 3, > pot_extrapolation = "second_order", > wfc_extrapolation = "second_order", > > I have done this relaxation at several values of celldm(3) to find the > ones that has minimum energy and zero stress. Let me to note that I > can use of vc-relax calculations for this purpose because celldm(1) is > fixed. For some values of celldm(3) every thing is OK and the system > relax well and both etot_conv_thr and forc_conv_thr satisfies. But in > some other values of celldm(3) the calculation stops with the > following error: > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from checkallsym : error # 1 > some of the original symmetry operations not satisfied > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > After more accurate consideration of the cases that have above error, > I found that in that cases, the relaxation procedure has been done > correctly for a few steps (2 - 3 step) and then in the last steps the > position of atoms in x and y directions also has changed while there > is no force in these two direction. But after that program has tried > to symmetrize the position and change back the value of x and y > positions as follows: > > ATOMIC_POSITIONS (alat) > Ga 0.000000000 0.000000000 0.000000000 > As 0.000000000 0.502872976 0.354710310 > Cr 0.502872976 0.502872976 0.686421612 > As 0.502872976 0.000000000 1.018132914 > > > SYMMETRIZED ATOMIC COORDINATES) > > ATOMIC_POSITIONS (alat) > Ga 0.000000000 0.000000000 0.000000000 > As 0.000000000 0.500000000 0.350788698 > Cr 0.500000000 0.500000000 0.682500000 > As 0.500000000 0.000000000 1.014211302 > > and then the above mentioned error occurs. It is the situation for all > the cases that relaxation has not been completed. > When I restarted one of this cases with damp method (instead of bfgs) > the above error did not appear and the system relaxed correctly. > > I would appreciate if some body explains why by using bfgs such errors > occurs and how I can solve that. Otherwise I should use the damp > method for relaxation that usually needs to more steps to reach to the > minimum energy. > > thanks in advance > Javad Hashemifar > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From jhashemifar at gmail.com Fri Dec 22 11:52:20 2006 From: jhashemifar at gmail.com (Javad hashemifar) Date: Fri, 22 Dec 2006 11:52:20 +0100 Subject: [Pw_forum] problem in relaxation by using bfgs In-Reply-To: <00c101c725af$e481ba00$1d00a8c0@solarflare> References: <2fb18d9f0612220020x36188117g36a386607ebfb157@mail.gmail.com> <00c101c725af$e481ba00$1d00a8c0@solarflare> Message-ID: <2fb18d9f0612220252m5376e78eia8596e709a03ced@mail.gmail.com> Thanks Huiqun for your kind answer. In fact I was using 2 processors for my job. But the interesting point is that when about 2 hours ago I repeated calculation of one case on 4 processors (with exactly the same input parameters as before) the mentioned error message did not appear any more and system relaxed completely and correctly. I will try to check the first_order extrapolation. Thanks again Javad Hashemifar On 12/22/06, Huiqun Zhou wrote: > Javad, > > I got the same problem several months before. In my case, I noticed that if > I > run my job on equal to or less than 2 processors (or CPU cores), it will be > OK. > > Another way to get rid of it is to comment out the pot and wfc > extrapolation. > Of course, this will slow down your calculation to some extent. > > I didn't try to use 'first_order', you may test this first. > > Huiqun > > > ----- Original Message ----- > From: "Javad hashemifar" > To: > Sent: Friday, December 22, 2006 4:20 PM > Subject: [Pw_forum] problem in relaxation by using bfgs > > > > Dear Pwscf users > > > > I am trying to relax a tetragonal interface supercell at different > > values of vertical lattice parameter (celldm(3)). I am using > > calculation=relax and the namelist IONS is as follows: > > > > ion_dynamic = bfgs > > bfgs_ndim = 3, > > pot_extrapolation = "second_order", > > wfc_extrapolation = "second_order", > > > > I have done this relaxation at several values of celldm(3) to find the > > ones that has minimum energy and zero stress. Let me to note that I > > can use of vc-relax calculations for this purpose because celldm(1) is > > fixed. For some values of celldm(3) every thing is OK and the system > > relax well and both etot_conv_thr and forc_conv_thr satisfies. But in > > some other values of celldm(3) the calculation stops with the > > following error: > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > from checkallsym : error # 1 > > some of the original symmetry operations not satisfied > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > After more accurate consideration of the cases that have above error, > > I found that in that cases, the relaxation procedure has been done > > correctly for a few steps (2 - 3 step) and then in the last steps the > > position of atoms in x and y directions also has changed while there > > is no force in these two direction. But after that program has tried > > to symmetrize the position and change back the value of x and y > > positions as follows: > > > > ATOMIC_POSITIONS (alat) > > Ga 0.000000000 0.000000000 0.000000000 > > As 0.000000000 0.502872976 0.354710310 > > Cr 0.502872976 0.502872976 0.686421612 > > As 0.502872976 0.000000000 1.018132914 > > > > > > SYMMETRIZED ATOMIC COORDINATES) > > > > ATOMIC_POSITIONS (alat) > > Ga 0.000000000 0.000000000 0.000000000 > > As 0.000000000 0.500000000 0.350788698 > > Cr 0.500000000 0.500000000 0.682500000 > > As 0.500000000 0.000000000 1.014211302 > > > > and then the above mentioned error occurs. It is the situation for all > > the cases that relaxation has not been completed. > > When I restarted one of this cases with damp method (instead of bfgs) > > the above error did not appear and the system relaxed correctly. > > > > I would appreciate if some body explains why by using bfgs such errors > > occurs and how I can solve that. Otherwise I should use the damp > > method for relaxation that usually needs to more steps to reach to the > > minimum energy. > > > > thanks in advance > > Javad Hashemifar > > _______________________________________________ > > 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 > -- ====================================== Seyed Javad Hashemifar, Ph.D. [current:] Tel:+49-203-3794743 Fax:+49-203-3794742 Fachbereich Physik (AG Kratzer), Universitat Duisburg-Essen 47048 Dusiburg, Germany [permanent:] Tel: +98-311-3912375 Fax: +98-311-3912376 Physics Department, Isfahan University of Technology 84156 Isfahan, Iran --------------------------------------------------------------------------- From giannozz at nest.sns.it Fri Dec 22 14:39:01 2006 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 22 Dec 2006 14:39:01 +0100 Subject: [Pw_forum] problem in relaxation by using bfgs In-Reply-To: <2fb18d9f0612220252m5376e78eia8596e709a03ced@mail.gmail.com> References: <2fb18d9f0612220020x36188117g36a386607ebfb157@mail.gmail.com> <00c101c725af$e481ba00$1d00a8c0@solarflare> <2fb18d9f0612220252m5376e78eia8596e709a03ced@mail.gmail.com> Message-ID: On Dec 22, 2006, at 11:52 , Javad hashemifar wrote: > In fact I was using 2 processors for my job. But the interesting > point is that when about 2 hours ago I repeated calculation of > one case on 4 processors (with exactly the same input parameters > as before) the mentioned error message did not appear any more > and system relaxed completely and correctly. could you please provide your job? Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From jhashemifar at gmail.com Fri Dec 22 16:28:39 2006 From: jhashemifar at gmail.com (Javad hashemifar) Date: Fri, 22 Dec 2006 16:28:39 +0100 Subject: [Pw_forum] problem in relaxation by using bfgs In-Reply-To: <2fb18d9f0612220654x440bdb27xc8097a1ecd69c598@mail.gmail.com> References: <2fb18d9f0612220020x36188117g36a386607ebfb157@mail.gmail.com> <00c101c725af$e481ba00$1d00a8c0@solarflare> <2fb18d9f0612220252m5376e78eia8596e709a03ced@mail.gmail.com> <2fb18d9f0612220654x440bdb27xc8097a1ecd69c598@mail.gmail.com> Message-ID: <2fb18d9f0612220728m39ee3f0do5ddda6a6e495f850@mail.gmail.com> Please find as an attachment my job file. The obtained output file by this job show that one more step is required for reaching to etot_conv_thr while forc_conv_thr is already satisfied. Thanks for your attention. Javad Hashemifar On 12/22/06, Paolo Giannozzi wrote: > > On Dec 22, 2006, at 11:52 , Javad hashemifar wrote: > > > In fact I was using 2 processors for my job. But the interesting > > point is that when about 2 hours ago I repeated calculation of > > one case on 4 processors (with exactly the same input parameters > > as before) the mentioned error message did not appear any more > > and system relaxed completely and correctly. > > could you please provide your job? Paolo > --- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ====================================== Seyed Javad Hashemifar, Ph.D. [current:] Tel:+49-203-3794743 Fax:+49-203-3794742 Fachbereich Physik (AG Kratzer), Universitat Duisburg-Essen 47048 Dusiburg, Germany [permanent:] Tel: +98-311-3912375 Fax: +98-311-3912376 Physics Department, Isfahan University of Technology 84156 Isfahan, Iran --------------------------------------------------------------------------- -- ====================================== Seyed Javad Hashemifar, Ph.D. [current:] Tel:+49-203-3794743 Fax:+49-203-3794742 Fachbereich Physik (AG Kratzer), Universitat Duisburg-Essen 47048 Dusiburg, Germany [permanent:] Tel: +98-311-3912375 Fax: +98-311-3912376 Physics Department, Isfahan University of Technology 84156 Isfahan, Iran --------------------------------------------------------------------------- -------------- next part -------------- A non-text attachment was scrubbed... Name: 1g-1c.job Type: application/octet-stream Size: 1602 bytes Desc: not available Url : /pipermail/attachments/20061222/f5b5b831/attachment.obj From wjhongxia at yahoo.com.cn Sun Dec 24 13:03:36 2006 From: wjhongxia at yahoo.com.cn (=?gb2312?q?=BD=AA=D0=A1=CD=F1=20=BD=AA?=) Date: Sun, 24 Dec 2006 20:03:36 +0800 (CST) Subject: [Pw_forum] Self-Interaction-Correction (SIC Message-ID: <20061224120336.59535.qmail@web15005.mail.cnb.yahoo.com> Dear users, I need include the Self-Interaction-Correction (SIC) in the calculation, and i found SIC need to be included by myself, but I'm a new user of pw. So can you help me? i'll be appreciate your help. yours sincerely, hongxia __________________________________________________ ??????????????? http://cn.mail.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061224/0299edad/attachment.htm From lawrence_lee_lee at yahoo.com.hk Mon Dec 25 05:13:55 2006 From: lawrence_lee_lee at yahoo.com.hk (Lawrence Lee) Date: Mon, 25 Dec 2006 12:13:55 +0800 (CST) Subject: [Pw_forum] =?big5?q?=A6^=C2=D0=A1G=20[Pw=5Fforum]=20Self-Interaction-Correction=20(S?= =?big5?q?IC?= In-Reply-To: <20061224120336.59535.qmail@web15005.mail.cnb.yahoo.com> Message-ID: <20061225041355.40580.qmail@web54405.mail.yahoo.com> ???p?? ?? ???G Dear users, I need include the Self-Interaction-Correction (SIC) in the calculation, and i found SIC need to be included by myself, but I'm a new user of pw. So can you help me? i'll be appreciate your help. yours sincerely, hongxia __________________________________________________ ????????????????????????????? http://cn.mail.yahoo.com _______________________________________ YM - ???u?T?? ?N???A?S???W???A?A???B?????i?H?d?U?T?????A?A???A?W?????N?????Y?????A???????????N?????C http://messenger.yahoo.com.hk -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061225/af93aee8/attachment.htm From ding at sissa.it Mon Dec 25 09:10:46 2006 From: ding at sissa.it (Xunlei Ding) Date: Mon, 25 Dec 2006 09:10:46 +0100 Subject: [Pw_forum] Self-Interaction-Correction (SIC In-Reply-To: <20061224120336.59535.qmail@web15005.mail.cnb.yahoo.com> References: <20061224120336.59535.qmail@web15005.mail.cnb.yahoo.com> Message-ID: <1167034246.458f8786dc4f1@webmail.sissa.it> Dear hongxia, When you generate PP, you can set "isic= 1" to include the SIC (see INPUT_LD1 in $espresso/atomic_doc). Maybe you can test some suitable PP including SIC if you can find some on Web. Yours, Ding Quoting ?????? ?? : > Dear users, > I need include the Self-Interaction-Correction (SIC) in the calculation, and > i found SIC need to be included by myself, but I'm a new user of pw. So can > you help me? i'll be appreciate your help. > yours sincerely, > hongxia > > __________________________________________________ > ????????????????????????????? > http://cn.mail.yahoo.com ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From emenendez at macul.ciencias.uchile.cl Tue Dec 26 01:20:02 2006 From: emenendez at macul.ciencias.uchile.cl (Eduardo Ariel Menendez P) Date: Mon, 25 Dec 2006 21:20:02 -0300 (CLST) Subject: [Pw_forum] questions on molecular dynamics example Message-ID: Hi Paolo, I saw these options in the examples of molecular dynamics woth PW. There is few information in the Doc files and the forum. pot_extrapolation='second-order', wfc_extrapolation='second-order', I guessed that extrapolation options would reduce the number of self-consistent steps in MD steps. However, in the case I am running (CdTe) he number of self consistent steps at each ionic steps averages 16, regardless of the extrapolation keywords. Other keyword that I see in the examples is disk_io='high',etc, Is this keyword useful to improve the efficiency of molecular dynamics? Other issue. I had this error in step 90 iteration # 4 ecut= 30.00 Ry beta=0.70 Davidson diagonalization with overlap %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from rdiaghg : error # 1986 info =/= 0 Consulting the manual and the forum I see that it is difficult to find the cause, and that the first choice is restart and see what happens. I did it and the calculation just continued without error. ?Does it allows to discard the possible cause of bad pseudopotential, and bug of the lapack algorithm, in favor of buggy mahine optimization of lapack (MKL) ? Thanks Eduardo Eduardo A. Menendez Proupin Department of Physics Faculty of Science University of Chile Las Palmeras 3425 ?u?oa, Santiago Chile Phone: 56+2+978 74 11 http://fisica.ciencias.uchile.cl/~emenendez/ From ding at sissa.it Wed Dec 27 10:55:43 2006 From: ding at sissa.it (Xunlei Ding) Date: Wed, 27 Dec 2006 10:55:43 +0100 Subject: [Pw_forum] questions on molecular dynamics example In-Reply-To: References: Message-ID: <1167213343.4592431f9cd4f@webmail.sissa.it> Dear Eduardo I am also interested in your questions. I think extrapolation will accelerate scf calculations in some cases, but not in all case. It is more suitable for the system in which the ionic positions change little between two MD steps or optimization steps in 'relax' calculations. Yours sincerely, Ding Quoting Eduardo Ariel Menendez P : > Hi Paolo, > I saw these options in the examples of molecular dynamics woth PW. There > is few information in the Doc files and the forum. > > pot_extrapolation='second-order', > wfc_extrapolation='second-order', > > I guessed that extrapolation options would reduce the number of > self-consistent steps in MD steps. However, in the case I am running > (CdTe) he number of self consistent steps at each ionic steps averages > 16, regardless of the extrapolation keywords. > > Other keyword that I see in the examples is > disk_io='high',etc, > Is this keyword useful to improve the efficiency of molecular dynamics? > > Other issue. I had this error in step 90 > iteration # 4 ecut= 30.00 Ry beta=0.70 > Davidson diagonalization with overlap > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from rdiaghg : error # 1986 > info =/= 0 > Consulting the manual and the forum I see that it is difficult to find > the cause, and that the first choice is restart > and see what happens. I did it and the calculation just continued without > error. ?Does it allows to discard the possible cause of bad > pseudopotential, and bug of the lapack algorithm, in favor of buggy mahine > optimization of lapack (MKL) ? > > Thanks > Eduardo > > Eduardo A. Menendez Proupin > Department of Physics > Faculty of Science > University of Chile > Las Palmeras 3425 > ?u?oa, Santiago > Chile > Phone: 56+2+978 74 11 > http://fisica.ciencias.uchile.cl/~emenendez/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From wlyim at puccini.che.pitt.edu Wed Dec 27 22:29:17 2006 From: wlyim at puccini.che.pitt.edu (wlyim at puccini.che.pitt.edu) Date: Wed, 27 Dec 2006 16:29:17 -0500 (EST) Subject: [Pw_forum] ph.x v3.2 on NEC SX-8 Message-ID: Dear Sir/Madam, I compiled espresso-3.2 on NEC SX-8. The scf and nscf calculations can be completed successfully, but a problem was encountered when ph.x started, which seemed to be related to do dmxc_spin set startup. The error message is as follows. ========================================================================= $ mpirun -np 2 ./ph.x -npool 2 -in Co.ph.1.in Program PHONON v.3.2 starts ... Today is 27Dec2006 at 22: 1: 8 Parallel version (MPI) Number of processors in use: 2 K-points division: npool = 2 Ultrasoft (Vanderbilt) Pseudopotentials Planes per process (thick) : nr3 = 36 npp = 36 ncplane = 600 Proc/ planes cols G planes cols G columns G Pool (dense grid) (smooth grid) (wavefct grid) 1 36 271 5907 36 187 3285 61 627 0 36 271 5907 36 187 3285 61 627 nbndx = 22 nbnd = 22 natomwfc = 12 npwx = 428 nelec = 18.00 nkb = 36 ngl = 245 Check: negative/imaginary core charge= -0.000009 0.000014 negative rho (up, down): 0.861E-04 0.000E+00 starting from an old run Doing now the calculation for q point nr 1 * 252 Floating-point zero divide PROG=funct.dmxc_spin ELN=1193(400091fb8) * 252 Floating-point zero divide PROG=funct.dmxc_spin ELN=1193(400091fb8) * 252 Floating-point zero divide PROG=funct.dmxc_spin ELN=1193(400091fb8) * 252 Floating-point zero divide PROG=funct.dmxc_spin ELN=1193(400091fb8) * 252 Floating-point zero divide PROG=funct.dmxc_spin ELN=1193(400091fb8) * 253 Invalid operation PROG=funct.dmxc_spin ELN=1193(400091fb8) * 252 Floating-point zero divide PROG=funct.dmxc_spin ELN=1193(400091fb8) * 253 Invalid operation PROG=funct.dmxc_spin ELN=1193(400091fb8) * 252 Floating-point zero divide PROG=funct.dmxc_spin ELN=1193(400091fb8) * 253 Invalid operation PROG=funct.dmxc_spin ELN=1193(400091fb8) * 252 Floating-point zero divide PROG=funct.dmxc_spin ELN=1193(400091fb8) * 253 Invalid operation PROG=funct.dmxc_spin ELN=1193(400091fb8) * 252 Floating-point zero divide PROG=funct.dmxc_spin ELN=1193(400091fb8) * 253 Invalid operation PROG=funct.dmxc_spin ELN=1193(400091fb8) * 252 Floating-point zero divide PROG=funct.dmxc_spin ELN=1193(400091fb8) * 253 Invalid operation PROG=funct.dmxc_spin ELN=1193(400091fb8) * 252 Floating-point zero divide PROG=funct.dmxc_spin ELN=1193(400091fb8) * 253 Invalid operation PROG=funct.dmxc_spin ELN=1193(400091fb8) * 252 Floating-point zero divide PROG=funct.dmxc_spin ELN=1193(400091fb8) * 253 Invalid operation PROG=funct.dmxc_spin ELN=1193(400091fb8) * 252 Floating-point zero divide PROG=funct.dmxc_spin ELN=1193(400091fb8) * 253 Invalid operation PROG=funct.dmxc_spin ELN=1193(400091fb8) * 252 Floating-point zero divide PROG=funct.dmxc_spin ELN=1193(400091fb8) * 252 Floating-point zero divide PROG=funct.dmxc_spin ELN=1193(400091fb8) * 253 Invalid operation PROG=funct.dmxc_spin ELN=1193(400091fb8) * 252 Floating-point zero divide PROG=funct.dmxc_spin ELN=1193(400091fb8) * 252 Floating-point zero divide PROG=funct.dmxc_spin ELN=1193(400091fb8) * 253 Invalid operation PROG=funct.dmxc_spin ELN=1193(400091fb8) * 252 Floating-point zero divide PROG=funct.dmxc_spin ELN=1193(400091fb8) * 252 Floating-point zero divide PROG=funct.dmxc_spin ELN=1193(400091fb8) * 253 Invalid operation PROG=funct.dmxc_spin ELN=1193(400091fb8) * 252 Floating-point zero divide PROG=funct.dmxc_spin ELN=1193(400091fb8) * 252 Floating-point zero divide PROG=funct.dmxc_spin ELN=1193(400091fb8) * 253 Invalid operation PROG=funct.dmxc_spin ELN=1193(400091fb8) * 252 Floating-point zero divide PROG=funct.dmxc_spin ELN=1193(400091fb8) * 253 Invalid operation PROG=funct.dmxc_spin ELN=1193(400091fb8) * 252 Floating-point zero divide PROG=funct.dmxc_spin ELN=1193(400091fb8) * 253 Invalid operation PROG=funct.dmxc_spin ELN=1193(400091fb8) * 252 Floating-point zero divide PROG=funct.dmxc_spin ELN=1193(400091fb8) * 253 Invalid operation PROG=funct.dmxc_spin ELN=1193(400091fb8) * 252 Floating-point zero divide PROG=funct.dmxc_spin ELN=1193(400091fb8) * 253 Invalid operation PROG=funct.dmxc_spin ELN=1193(400091fb8) * 252 Floating-point zero divide PROG=funct.dmxc_spin ELN=1193(400091fb8) * 253 Invalid operation PROG=funct.dmxc_spin ELN=1193(400091fb8) * 252 Floating-point zero divide PROG=funct.dmxc_spin ELN=1193(400091fb8) * 253 Invalid operation PROG=funct.dmxc_spin ELN=1193(400091fb8) * 252 Floating-point zero divide PROG=funct.dmxc_spin ELN=1193(400091fb8) * 253 Invalid operation PROG=funct.dmxc_spin ELN=1193(400091fb8) * 252 Floating-point zero divide PROG=funct.dmxc_spin ELN=1193(400091fb8) * 253 Invalid operation PROG=funct.dmxc_spin ELN=1193(400091fb8) **** 99 Execution suspended PROG=funct.dmxc_spin ELN=1193(400091fb8) * 252 Floating-point zero divide PROG=funct.dmxc_spin ELN=1193(400091fb8) Called from phq_setup ELN=175(40027af54) Called from phonon ELN=264(4000027a8) * 252 Floating-point zero divide PROG=funct.dmxc_spin ELN=1193(400091fb8) ./ph.x(lang:f90): signal trap(SIGTERM: Software termination) v00: mpid: MPI process (universe = 0, rank = 1) terminated by exit(2) v00: mpid: MPI process (universe = 0, rank = 0) terminated by exit(1) $ ======================================================================= I am also attaching the make.sys file below. ===================================================================== # System-dependent definitions for NEC SX6 - Contributed by Guido Roma # Edit according to your needs .SUFFIXES : .SUFFIXES : .o .c .f .f90 .f90.o: $(CPP) $(CPPFLAGS) $*.f90 $*.F90 $(F90) $(F90FLAGS) -c $*.F90 -o $*.o .f.o: $(F77) $(FFLAGS) -c $< .c.o: $(CC) $(CFLAGS) -c $< MAKE = sxmake CPP = /SX/usr/lib/sxcpp DFLAGS = -P -E -DASL -D__USE_3D_FFT -DHAS_ZHEGVX -DLANGUAGE_FORTRAN -D__SX6 -USX -D__MPI -D__PARA ## For libfft library, part of Mathkeisan Libraries #DFLAGS = -P -E -DHAS_ZHEGVX -DLANGUAGE_FORTRAN -D__SX6 ## For libjmfft library (www.idris.fr) by Jean-Marie Teuler #DFLAGS = -P -E -DZZFFT3D=ccfft3d -DHAS_ZHEGVX -DLANGUAGE_FORTRAN -D__SX6 FDFLAGS = $(DFLAGS) IFLAGS = -I../include MODFLAGS = -I. -I../Modules -I../PW -I../PH -I../iotk/src LIBOBJS = ../flib/ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a # For fft routines of ASL library CPPFLAGS = $(DFLAGS) $(IFLAGS) HOST = -sx8 BASIC = -float0 -P stack $(HOST) -USX MISC = -eab -R5 -Wf" -P nh -ptr byte" -Wf,"-Ncont -A dbl4" MISC1 = -eab -R5 -Wf" -P nh -ptr byte" -Wf,"-cont -A dbl4" PROF = -p FTRACE = -ftrace OPT = -C hopt -Wf" -pvctl noifopt loopcnt=9999999 expand=12 fullmsg vwork=stack -fusion -O noif" OPTVSAFE = -C vsafe -Wf" -pvctl loopcnt=9999999 fullmsg vwork=stack " OPT0 = -C debug DEBUG = -g DEBUGOPT = -Wf" -init stack=zero heap=zero" # CC = sxc++ CC = sxcc CCLOCAL = cc F90 = sxmpif90 MPIF90 = sxmpif90 F77 = sxmpif90 MPIF77 = sxmpif90 FFLAGS = -f0 $(BASIC) $(MISC) $(OPT) $(DEBUGOPT) # $(FTRACE) # FFLAGS = -f0 $(BASIC) $(MISC) $(DEBUG) $(DEBUGOPT) $(OPT0) # FCAUTIOUS = -f0 $(BASIC) $(MISC1) $(DEBUG) $(DEBUGOPT) F90FLAGS = $(BASIC) $(MISC) $(OPT) $(DEBUGOPT) $(IFLAGS) $(MODFLAGS) # CFLAGS = -DLANGUAGE_C -DNEC -DSX -I$(INC_DIR) -hfloat0,0,acct CFLAGS = -D__SX6 $(IFLAGS) $(MODFLAGS) -D__MPI -D__PARA # With ASL fft libraries (and libfft for CP crayfft.f90) LIBS = -llapack -lblas -lasl -lfft ## With libfft (Mathkeisan) libraries ## be careful, versions <= 1.4 are buggy (zzfft3d), ##wait for 1.5 (expected end of 2003) # LIBS = -llapack -lblas ../zzfft3d.o -lfft ## You can find the jmfft Cray compatible library written ## by Jean-Marie Teuler on www.idris.fr (search for jmfft) # LIBS = -llapack -lblas -L$(HOME)/mylocal/lib -ljmfft LD = $(MPIF90) # LDFLAGS = $(BASIC) $(PROF) $(FTRACE) LDFLAGS = $(BASIC) $(DEBUG) $(DEBUGOPT) \ -p # -p -Wl" -f zero " AR = sxar -ruvs ARFLAGS = RANLIB = echo ================================================================================= I will be very apprecated if somebody can help. Many thanks in advance. Best regards, William -- Dr. Wai-Leung Yim Institut fuer Reine und Angewandte Chemie, Theoretische Chemie, Carl von Ossiezky Universtaet Oldenburg, 26129 Oldenburg, Germany Email: wlyim at puccini.che.pitt.edu Phone: +49-441-798-3950 (office) Fax: +49-441-798-3964 From akohlmey at cmm.chem.upenn.edu Wed Dec 27 23:04:40 2006 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 27 Dec 2006 17:04:40 -0500 Subject: [Pw_forum] questions on molecular dynamics example In-Reply-To: References: Message-ID: <7b6913e90612271404v2d4646fai5beaf762dbb1fc15@mail.gmail.com> On 12/25/06, Eduardo Ariel Menendez P wrote: > Hi Paolo, > I saw these options in the examples of molecular dynamics woth PW. There > is few information in the Doc files and the forum. > > pot_extrapolation='second-order', > wfc_extrapolation='second-order', > > I guessed that extrapolation options would reduce the number of > self-consistent steps in MD steps. However, in the case I am running > (CdTe) he number of self consistent steps at each ionic steps averages > 16, regardless of the extrapolation keywords. > > Other keyword that I see in the examples is > disk_io='high',etc, > Is this keyword useful to improve the efficiency of molecular dynamics? that depends on the individual example and hardware. with a higher disk_io level, more data is written to disk and re-read instead of being kept in memory. if you have a lot of memory, a lower disk_io level should be better. in fact, for some machines with no local disk storage, it would be nice of have a disk_io level of 'no', i.e. keep everything in memory... > > Other issue. I had this error in step 90 > iteration # 4 ecut= 30.00 Ry beta=0.70 > Davidson diagonalization with overlap > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from rdiaghg : error # 1986 > info =/= 0 did you try changing the diagonalizer? > Consulting the manual and the forum I see that it is difficult to find > the cause, and that the first choice is restart > and see what happens. I did it and the calculation just continued without > error. ?Does it allows to discard the possible cause of bad > pseudopotential, and bug of the lapack algorithm, in favor of buggy mahine > optimization of lapack (MKL) ? i don't think that you have a buggy MKL. it might just be, that it get fed an input that it cannot converge. the fact that you do not see any improvements from wavefunction extrapolations could indicate that the order of your states keeps changing a lot and perhaps the davidson implementation is more sensitive there. (note: i'm not an expert here, but currently trying to learn about the details of these issues myself). i noticed however, that with different lapack implementations, this kind of error message keeps popping up more or less often (e.g. more often with ATLAS than with ACML than with MKL). also the compiler seems to have some impact, so it might be that very small differences in accuracy may have a large impact here (which would make it difficult to rule out all other possible sources of problems like suboptimal pseudopotentials, as they tend to enhance existing accuracy problems...). ciao, axel. > > Thanks > Eduardo > > Eduardo A. Menendez Proupin > Department of Physics > Faculty of Science > University of Chile > Las Palmeras 3425 > ?u?oa, Santiago > Chile > Phone: 56+2+978 74 11 > http://fisica.ciencias.uchile.cl/~emenendez/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From jhashemifar at gmail.com Thu Dec 28 09:25:17 2006 From: jhashemifar at gmail.com (Javad hashemifar) Date: Thu, 28 Dec 2006 09:25:17 +0100 Subject: [Pw_forum] stress or total energy Message-ID: <2fb18d9f0612280025t68cdf9b6n2308241b0e75e984@mail.gmail.com> Dear PWscf users I am trying to relax the c lattice parameter of a tetragonal supercell that its a lattice parameter is fixed to some experimental value. Therefore I am calculating this supercell at different values of c (celldm(3)) and looking at the total energy and stress. My feeling is that these two parameter should have consistent behavior and both could be used to find the optimized c. I mean I expect that when total energy is minimized, then the stress should vanish but it is not the case for my calculation and I observe that when the total energy is minimum, there is considerable value of stress (~ -10 kbar) in the system. I would appreciate if some body explain what is the problem and if it is really true that stress and total energy have not the same behavior, which one should be used to find out relaxed lattice parameters. I expect that total energy is the main criteria for relaxation of the lattice parameters ?? Best regards Javad Hashemifar On 12/27/06, Axel Kohlmeyer wrote: > On 12/25/06, Eduardo Ariel Menendez P > wrote: > > Hi Paolo, > > I saw these options in the examples of molecular dynamics woth PW. There > > is few information in the Doc files and the forum. > > > > pot_extrapolation='second-order', > > wfc_extrapolation='second-order', > > > > I guessed that extrapolation options would reduce the number of > > self-consistent steps in MD steps. However, in the case I am running > > (CdTe) he number of self consistent steps at each ionic steps averages > > 16, regardless of the extrapolation keywords. > > > > Other keyword that I see in the examples is > > disk_io='high',etc, > > Is this keyword useful to improve the efficiency of molecular dynamics? > > that depends on the individual example and hardware. > with a higher disk_io level, more data is written to disk > and re-read instead of being kept in memory. if you have > a lot of memory, a lower disk_io level should be better. > in fact, for some machines with no local disk storage, > it would be nice of have a disk_io level of 'no', i.e. keep > everything in memory... > > > > > Other issue. I had this error in step 90 > > iteration # 4 ecut= 30.00 Ry beta=0.70 > > Davidson diagonalization with overlap > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > from rdiaghg : error # 1986 > > info =/= 0 > > > did you try changing the diagonalizer? > > > Consulting the manual and the forum I see that it is difficult to find > > the cause, and that the first choice is restart > > and see what happens. I did it and the calculation just continued without > > error. ?Does it allows to discard the possible cause of bad > > pseudopotential, and bug of the lapack algorithm, in favor of buggy mahine > > optimization of lapack (MKL) ? > > i don't think that you have a buggy MKL. it might just be, that it get fed an > input that it cannot converge. the fact that you do not see any improvements > from wavefunction extrapolations could indicate that the order of your states > keeps changing a lot and perhaps the davidson implementation is more > sensitive there. > (note: i'm not an expert here, but currently trying to learn about the details > of these issues myself). > > i noticed however, that with different lapack implementations, this kind of > error message keeps popping up more or less often (e.g. more often with > ATLAS than with ACML than with MKL). also the compiler seems to have > some impact, so it might be that very small differences in accuracy may > have a large impact here (which would make it difficult to rule out all other > possible sources of problems like suboptimal pseudopotentials, as they > tend to enhance existing accuracy problems...). > > ciao, > axel. > > > > > Thanks > > Eduardo > > > > Eduardo A. Menendez Proupin > > Department of Physics > > Faculty of Science > > University of Chile > > Las Palmeras 3425 > > ?u?oa, Santiago > > Chile > > Phone: 56+2+978 74 11 > > http://fisica.ciencias.uchile.cl/~emenendez/ > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > -- > ======================================================================= > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu > Center for Molecular Modeling -- University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 > ======================================================================= > If you make something idiot-proof, the universe creates a better idiot. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ====================================== Seyed Javad Hashemifar, Ph.D. [current:] Tel:+49-203-3794743 Fax:+49-203-3794742 Fachbereich Physik (AG Kratzer), Universitat Duisburg-Essen 47048 Dusiburg, Germany [permanent:] Tel: +98-311-3912375 Fax: +98-311-3912376 Physics Department, Isfahan University of Technology 84156 Isfahan, Iran --------------------------------------------------------------------------- From katalin.gaal-nagy at physik.uni-regensburg.de Thu Dec 28 11:18:55 2006 From: katalin.gaal-nagy at physik.uni-regensburg.de (Katalin Gaal-Nagy) Date: Thu, 28 Dec 2006 11:18:55 +0100 (CET) Subject: [Pw_forum] stress or total energy In-Reply-To: <2fb18d9f0612280025t68cdf9b6n2308241b0e75e984@mail.gmail.com> References: <2fb18d9f0612280025t68cdf9b6n2308241b0e75e984@mail.gmail.com> Message-ID: Dear Javad, one reason for the discrepancy could be that you are not converged enough with respect to the number of plane waves, since the stress is very sensitive to that quantity. If you have calculated also the stress during your convergence tests with respect to the ecut, you can estimate the error in the stress. Of course one expects that the stress vanishes at the minimum of the total energy. Another reason coul be that you are using the experimental lattice constant, which could yield a energy which is not at the minimum of the total energy due to the over/underestimation of the lattice constant using LDA/GGA. Thus, I suggest to relax also the lattice constant together with the c/a in order to obtain the values at the energy minimum of your calculation. However, 10 kbar is a rather small value which could be somehow acceptable. But maybe someone else could give you further hints. Best wishes, Katalin On Thu, 28 Dec 2006, Javad hashemifar wrote: > Dear PWscf users > > I am trying to relax the c lattice parameter of a tetragonal supercell > that its a lattice parameter is fixed to some experimental value. > Therefore I am calculating this supercell at different values of c > (celldm(3)) and looking at the total energy and stress. > My feeling is that these two parameter should have consistent behavior > and both could be used to find the optimized c. I mean I expect that > when total energy is minimized, then the stress should vanish but it > is not the case for my calculation and I observe that when the total > energy is minimum, there is considerable value of stress (~ -10 kbar) > in the system. > I would appreciate if some body explain what is the problem and > if it is really true that stress and total energy have not the same > behavior, which one should be used to find out relaxed lattice > parameters. I expect that total energy is the main criteria for > relaxation of the lattice parameters ?? > > Best regards > Javad Hashemifar > From emenendez at macul.ciencias.uchile.cl Thu Dec 28 11:35:49 2006 From: emenendez at macul.ciencias.uchile.cl (Eduardo Ariel Menendez P) Date: Thu, 28 Dec 2006 07:35:49 -0300 (CLST) Subject: [Pw_forum] questions on molecular dynamics example In-Reply-To: <20061228063758.32036.28560.Mailman@democritos.sissa.it> References: <20061228063758.32036.28560.Mailman@democritos.sissa.it> Message-ID: Wow!! You are not taking hollidays yet! Thanks for your cooperation. I have rather low memory, then maybe disk_io is good for me. Regarding the wfc extrapolation, I just realize that I am doing velocity rescaling at every ionic step, hence a 'second order ' extrapolation would be fooled. However, I don not understand why in the example 4 I do not see differences between the use of extrrapolation or commenting it. > From: "Axel Kohlmeyer" > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] questions on molecular dynamics example > Reply-To: pw_forum at pwscf.org > > On 12/25/06, Eduardo Ariel Menendez P > wrote: > > Hi Paolo, > > I saw these options in the examples of molecular dynamics woth PW. There > > is few information in the Doc files and the forum. > > > > pot_extrapolation=3D'second-order', > > wfc_extrapolation=3D'second-order', > > > > I guessed that extrapolation options would reduce the number of > > self-consistent steps in MD steps. However, in the case I am running > > (CdTe) he number of self consistent steps at each ionic steps averages > > 16, regardless of the extrapolation keywords. > > > > Other keyword that I see in the examples is > > disk_io=3D'high',etc, > > Is this keyword useful to improve the efficiency of molecular dynamics? > > that depends on the individual example and hardware. > with a higher disk_io level, more data is written to disk > and re-read instead of being kept in memory. if you have > a lot of memory, a lower disk_io level should be better. > in fact, for some machines with no local disk storage, > it would be nice of have a disk_io level of 'no', i.e. keep > everything in memory... > > > > > Other issue. I had this error in step 90 > > iteration # 4 ecut=3D 30.00 Ry beta=3D0.70 > > Davidson diagonalization with overlap > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%= > %%%%% > > from rdiaghg : error # 1986 > > info =3D/=3D 0 > > > did you try changing the diagonalizer? > > > Consulting the manual and the forum I see that it is difficult to find > > the cause, and that the first choice is restart > > and see what happens. I did it and the calculation just continued without > > error. ?Does it allows to discard the possible cause of bad > > pseudopotential, and bug of the lapack algorithm, in favor of buggy mahin= > e > > optimization of lapack (MKL) ? > > i don't think that you have a buggy MKL. it might just be, that it get fed = > an > input that it cannot converge. the fact that you do not see any improvement= > s > from wavefunction extrapolations could indicate that the order of your stat= > es > keeps changing a lot and perhaps the davidson implementation is more > sensitive there. > (note: i'm not an expert here, but currently trying to learn about the deta= > ils > of these issues myself). > > i noticed however, that with different lapack implementations, this kind of > error message keeps popping up more or less often (e.g. more often with > ATLAS than with ACML than with MKL). also the compiler seems to have > some impact, so it might be that very small differences in accuracy may > have a large impact here (which would make it difficult to rule out all oth= > er > possible sources of problems like suboptimal pseudopotentials, as they > tend to enhance existing accuracy problems...). > > ciao, > axel. > > > > > Thanks > > Eduardo > > > > Eduardo A. Menendez Proupin > > Department of Physics > > Faculty of Science From s305igun at mail.chem.itb.ac.id Thu Dec 28 14:25:23 2006 From: s305igun at mail.chem.itb.ac.id (Rahmat Gunawan) Date: Thu, 28 Dec 2006 20:25:23 +0700 (WIT) Subject: [Pw_forum] [Pw_forum]: Marry X-Mas and Happy New Year 2007 In-Reply-To: References: <20061228063758.32036.28560.Mailman@democritos.sissa.it> Message-ID: <1064.167.205.72.49.1167312323.squirrel@webmail.chem.itb.ac.id> Dear PW_Forum For all Quantum Espresso-PWscf-PWgui-XCrySDen Users.... I would like to say: ************************************************************************* ************************************************************************* ============== MARRY X-MAS AND HAPPY NEW YEAR 2007 ================ ************************************************************************* ************************************************************************* Success for your excellent research Thanks for your help Sincerely Yours Rahmat Gunawan Chemistry Student Lab. of Theoretical and Computational Chemistry Dept. of Chemistry Faculty of Mathematics and Natural Sciences Bandung Institute of Technology West Java Indonesia From akohlmey at cmm.chem.upenn.edu Thu Dec 28 19:08:23 2006 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Thu, 28 Dec 2006 13:08:23 -0500 (EST) Subject: [Pw_forum] ph.x v3.2 on NEC SX-8 In-Reply-To: Message-ID: On Wed, 27 Dec 2006 wlyim at puccini.che.pitt.edu wrote: WY> Dear Sir/Madam, WY> WY> I compiled espresso-3.2 on NEC SX-8. The scf and nscf calculations can be WY> completed successfully, but a problem was encountered when ph.x started, WY> which seemed to be related to do dmxc_spin set startup. The error message WY> is as follows. thanks for the report. can you please check whether you can reproduce this error with one of the examples shipped with the distribution. there are a number of reasons why this may happen. so it would be useful to reduce the number of unknowns (input and pseudopotetial files). thanks, 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 emenendez at macul.ciencias.uchile.cl Thu Dec 28 18:21:29 2006 From: emenendez at macul.ciencias.uchile.cl (Eduardo Ariel Menendez P) Date: Thu, 28 Dec 2006 14:21:29 -0300 (CLST) Subject: [Pw_forum] questions on molecular dynamics example In-Reply-To: References: <20061228063758.32036.28560.Mailman@democritos.sissa.it> Message-ID: Hi everybody, I think that now I understand the usefulness of extrapolation. Default options are pot_extrapolation='atomic', wfc_extrapolation='none' I think that wfc_extrapolation acts only for the first self-consistent iteration at any ionic configuration, i.e., the guess wfc is taken from the converged wfc at the previous ionic config, and extrapolated using some differential formula. Its use is to accelerate the first scf iteration. Once the first iteration is completed, the wfc is the same either if extrapolation is used or not (if it is converged). Hence, the guess wfc for the second iteration is always the one that satisfy the KS equation for the guess potential. Hence, wfc_extrapolation does not affect the number of scf iterations. pot_extrapolation influences the guess for the potential, then it has a direct influence on the number of iterations needed for self-consistency. Here I assume that the default value is very good and is almost equivalent to using the second order extrapolation (at least for my insulating system and for the example 4). I have just made a test calculation (verlet dynamics, no T rescaling) using pot_extrapolation='none' and the number of scf iterations for convergence increases. Please, correct me if this is not true. It left to find out if the acceleration of the firs scf iteration mades a big difference in the total CPU time. Best regards Happy 2007 Eduardo > > Wow!! You are not taking hollidays yet! Thanks for your cooperation. > I have rather low memory, then maybe disk_io is good for me. > Regarding the wfc extrapolation, I just realize that I am doing velocity > rescaling at every ionic step, hence a 'second order ' extrapolation would > be fooled. However, I don not understand why in the example 4 I do not see > differences between the use of extrrapolation or commenting it. > > > From: "Axel Kohlmeyer" > > To: pw_forum at pwscf.org > > Subject: Re: [Pw_forum] questions on molecular dynamics example > > Reply-To: pw_forum at pwscf.org > > > > On 12/25/06, Eduardo Ariel Menendez P > > wrote: > > > Hi Paolo, > > > I saw these options in the examples of molecular dynamics woth PW. There > > > is few information in the Doc files and the forum. > > > > > > pot_extrapolation=3D'second-order', > > > wfc_extrapolation=3D'second-order', > > > > > > I guessed that extrapolation options would reduce the number of > > > self-consistent steps in MD steps. However, in the case I am running > > > (CdTe) he number of self consistent steps at each ionic steps averages > > > 16, regardless of the extrapolation keywords. > > > > > > Other keyword that I see in the examples is > > > disk_io=3D'high',etc, > > > Is this keyword useful to improve the efficiency of molecular dynamics? > > > > that depends on the individual example and hardware. > > with a higher disk_io level, more data is written to disk > > and re-read instead of being kept in memory. if you have > > a lot of memory, a lower disk_io level should be better. > > in fact, for some machines with no local disk storage, > > it would be nice of have a disk_io level of 'no', i.e. keep > > everything in memory... > > > > > > > > Other issue. I had this error in step 90 > > > iteration # 4 ecut=3D 30.00 Ry beta=3D0.70 > > > Davidson diagonalization with overlap > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%= > > %%%%% > > > from rdiaghg : error # 1986 > > > info =3D/=3D 0 > > > > > > did you try changing the diagonalizer? > > > > > Consulting the manual and the forum I see that it is difficult to find > > > the cause, and that the first choice is restart > > > and see what happens. I did it and the calculation just continued without > > > error. ?Does it allows to discard the possible cause of bad > > > pseudopotential, and bug of the lapack algorithm, in favor of buggy mahin= > > e > > > optimization of lapack (MKL) ? > > > > i don't think that you have a buggy MKL. it might just be, that it get fed = > > an > > input that it cannot converge. the fact that you do not see any improvement= > > s > > from wavefunction extrapolations could indicate that the order of your stat= > > es > > keeps changing a lot and perhaps the davidson implementation is more > > sensitive there. > > (note: i'm not an expert here, but currently trying to learn about the deta= > > ils > > of these issues myself). > > > > i noticed however, that with different lapack implementations, this kind of > > error message keeps popping up more or less often (e.g. more often with > > ATLAS than with ACML than with MKL). also the compiler seems to have > > some impact, so it might be that very small differences in accuracy may > > have a large impact here (which would make it difficult to rule out all oth= > > er > > possible sources of problems like suboptimal pseudopotentials, as they > > tend to enhance existing accuracy problems...). > > > > ciao, > > axel. > > > > > > > > Thanks > > > Eduardo > > > > > > Eduardo A. Menendez Proupin > > > Department of Physics > > > Faculty of Science > From wlyim at puccini.che.pitt.edu Thu Dec 28 23:00:41 2006 From: wlyim at puccini.che.pitt.edu (wlyim at puccini.che.pitt.edu) Date: Thu, 28 Dec 2006 17:00:41 -0500 (EST) Subject: [Pw_forum] ph.x v3.2 on NEC SX-8 In-Reply-To: Message-ID: Thanks for your suggestion. I will try one of the examples as soon as possible. Current status: ifort-compiled pw.x and ph.x can complete the job normally. However, the NEC executables pass a larger "nrxx" value, 22200 in NEC vs 20736 in Intel, given that nr1=24,nr2=24,nr3=36. So in NEC, some zero "zeta" were passed to dmxc_spin subroutine which led to "divide by zero" error at line 1192 in Modules/functionals.f90. Interestingly, pw.x by sxcross compiler and ifort gave the same scf results, while ph.x in NEC didn't work... Any suggestion is welcome, e.g. compiler options, preprocessor flags... Best regards, William On Thu, 28 Dec 2006, Axel Kohlmeyer wrote: > On Wed, 27 Dec 2006 wlyim at puccini.che.pitt.edu wrote: > > WY> Dear Sir/Madam, > WY> > WY> I compiled espresso-3.2 on NEC SX-8. The scf and nscf calculations can be > WY> completed successfully, but a problem was encountered when ph.x started, > WY> which seemed to be related to do dmxc_spin set startup. The error message > WY> is as follows. > > thanks for the report. > can you please check whether you can reproduce this error > with one of the examples shipped with the distribution. > > there are a number of reasons why this may happen. so it > would be useful to reduce the number of unknowns (input and > pseudopotetial files). > > thanks, > axel. > > > -- Dr. Wai-Leung Yim Institut fuer Reine und Angewandte Chemie, Theoretische Chemie, Carl von Ossiezky Universtaet Oldenburg, 26129 Oldenburg, Germany Email: wlyim at puccini.che.pitt.edu Phone: +49-441-798-3950 (office) +49-441-798-5102 (home) Fax: +49-441-798-3964 From akohlmey at cmm.chem.upenn.edu Fri Dec 29 00:49:29 2006 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Thu, 28 Dec 2006 18:49:29 -0500 Subject: [Pw_forum] ph.x v3.2 on NEC SX-8 In-Reply-To: References: Message-ID: <7b6913e90612281549u28003c6dqcda7ca1748fbb433@mail.gmail.com> On 12/28/06, wlyim at puccini.che.pitt.edu wrote: > Thanks for your suggestion. I will try one of the examples as soon as > possible. > > Current status: ifort-compiled pw.x and ph.x can complete the job > normally. However, the NEC executables pass a larger "nrxx" value, 22200 > in NEC vs 20736 in Intel, given that nr1=24,nr2=24,nr3=36. So in NEC, some that is very interesting. > zero "zeta" were passed to dmxc_spin subroutine which led to "divide by > zero" error at line 1192 in Modules/functionals.f90. Interestingly, pw.x > by sxcross compiler and ifort gave the same scf results, while ph.x in NEC > didn't work... no surprise here. pw.x does not need the derivatives of the exchange- correlation potential. > Any suggestion is welcome, e.g. compiler options, preprocessor flags... from looking at the code it seems that the relation nrxx=nrx1*nrx2*nrx3 is only true in the serial case. see Modules/fft_types.f90 lines 242ff. the intel compiler code usually continues with a denormalized number (NaN or Inf) after a division by zero (same as IBM xlf) and since the corresponding grid point is not accessed this does not propagate. to remedy the situation you can try a) compile a serial version of the code, b) look for a compiler flag to continue after a denormalized number, or c) correct the code in PH/phq_setup.f90 to call dmxc()/dmxc_spin() only for values or 'ir' that correspond to valid grid points. cheers, axel. > > Best regards, > William > -- ======================================================================= 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 naromero at gmail.com Fri Dec 29 16:15:10 2006 From: naromero at gmail.com (Nichols A. Romero) Date: Fri, 29 Dec 2006 10:15:10 -0500 Subject: [Pw_forum] stress or total energy In-Reply-To: References: <2fb18d9f0612280025t68cdf9b6n2308241b0e75e984@mail.gmail.com> Message-ID: <6ac064b60612290715k15d6240m6f179c1642a9d983@mail.gmail.com> Javad, It is unlikely that you can converge the stress more than a couple of kilobar. (It is calculated in a complete different way than in classical MD.) As hinted at in the previous e-mail, the pressure will converge slower than the energy within the PW pseudopotential scheme. In other words, if the calculation needs only 40 Ry to converge the energy well, don't be surprised if you have to go 60 - 80 Ry to converge you stress tensor. You can also calculate the pressure (roughly) as P = -dE/dV where E and V are the total energy and volume. You would need to work out the unit conversion to kbar. It is good to look back in the literature to papers that discuss this matter in more detail: Phys. Rev. B 32, 3780 (1985). Phys. Rev. B 52, 8160 (1995). On 12/28/06, Katalin Gaal-Nagy wrote: > > Dear Javad, > > one reason for the discrepancy could be that you are not converged enough > with respect to the number of plane waves, since the stress is very > sensitive to that quantity. If you have calculated also the stress during > your convergence tests with respect to the ecut, you can estimate the > error in the stress. > Of course one expects that the stress vanishes at the minimum of the total > energy. > > Another reason coul be that you are using the experimental lattice > constant, which could yield a energy which is not at the minimum of the > total energy due to the over/underestimation of the lattice constant using > LDA/GGA. Thus, I suggest to relax also the lattice constant together with > the c/a in order to obtain the values at the energy minimum of your > calculation. > > However, 10 kbar is a rather small value which could be somehow > acceptable. > > But maybe someone else could give you further hints. > > Best wishes, > Katalin > > On Thu, 28 Dec 2006, Javad hashemifar wrote: > > > Dear PWscf users > > > > I am trying to relax the c lattice parameter of a tetragonal supercell > > that its a lattice parameter is fixed to some experimental value. > > Therefore I am calculating this supercell at different values of c > > (celldm(3)) and looking at the total energy and stress. > > My feeling is that these two parameter should have consistent behavior > > and both could be used to find the optimized c. I mean I expect that > > when total energy is minimized, then the stress should vanish but it > > is not the case for my calculation and I observe that when the total > > energy is minimum, there is considerable value of stress (~ -10 kbar) > > in the system. > > I would appreciate if some body explain what is the problem and > > if it is really true that stress and total energy have not the same > > behavior, which one should be used to find out relaxed lattice > > parameters. I expect that total energy is the main criteria for > > relaxation of the lattice parameters ?? > > > > Best regards > > Javad Hashemifar > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Nichols A. Romero, Ph.D. 1613 Denise Dr. Apt. D Forest Hill, MD 21050 443-567-8328 (C) 410-306-0709 (O) -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20061229/36d1ad47/attachment.htm From wlyim at puccini.che.pitt.edu Fri Dec 29 17:02:01 2006 From: wlyim at puccini.che.pitt.edu (wlyim at puccini.che.pitt.edu) Date: Fri, 29 Dec 2006 11:02:01 -0500 (EST) Subject: [Pw_forum] ph.x v3.2 on NEC SX-8 In-Reply-To: <7b6913e90612281549u28003c6dqcda7ca1748fbb433@mail.gmail.com> Message-ID: Thank Axel for fruitful discussion. The larger nrxx index in NEC is come from the "good_fft_dimension" subroutine, and nrxx=25x24x37 (=22200), instead of 24x24x36 in INTEL. I found that I cannot simply neglect the "zero" elements after I tried two things: 1. masked the overflow error can pass through the phq_setup step, but after the whole phonon cycles, it hanged at some point; 2. modified the dmxc_spin subroutine and kept the extra array zero. The program can run till the end but the result was wrong. Till now, I cannot find a way to solve the ph.x problem in NEC (pw.x works). I will be appreciated if someone will address this issue. Alternatively, I compiled espresso-2.1.4 in NEC using the following makefile, using the internal FFTW and __INTEL and __LINUX64 flags. On my test case, both pw.x and ph.x worked properly. ======================================================================== OSHOME=/nfs/home5/HLRS/xol/xolwlyim/PWSCF.2.1.4/espresso-2.1.4.parallel # # System-dependent definitions for NEC SX6 - Contributed by Guido Roma # Edit according to your needs # # Precompiler: # MAKE=sxmake CPP = /SX/usr/lib/sxcpp INC_DIR = ../include # For fft routines of ASL library CPPFLAGS = -P -E -DLANGUAGE_FORTRAN -D__INTEL -D__LINUX64 -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA -I$(INC_DIR) # For libfft library, part of Mathkeisan Libraries #CPPFLAGS = -P -E -DLANGUAGE_FORTRAN -DHAS_ZHEGVX -D__SX6 -I$(INC_DIR) # For libjmfft library (www.idris.fr) by Jean-Marie Teuler #CPPFLAGS = -P -E -DZZFFT3D=ccfft3d -DHAS_ZHEGVX -DLANGUAGE_FORTRAN -D__SX6 -I$(INC_DIR) HOST=-sx8 BASIC=-float0 -P stack $(HOST) MISC = -I$(INC_DIR) -eab -R5 -Wf" -P nh -ptr byte" -Wf,"-Ncont -A dbl4 " MISC1 = -I$(INC_DIR) -eab -R5 -Wf" -P nh -ptr byte" -Wf,"-cont -A dbl4 " PROF=-p FTRACE=-ftrace OPT= -C hopt -Wf" -pvctl noifopt loopcnt=9999999 expand=12 fullmsg vwork=stack -fusion -O noif" OPTVSAFE= -C vsafe -Wf" -pvctl loopcnt=9999999 fullmsg vwork=stack " OPT0= -C debug DEBUG= -g DEBUGOPT= -Wf" -init stack=zero heap=zero" # AR = sxar ARFLAGS = rv # This is needed to tell the compiler where modules are # MODULEFLAG= -I$(OSHOME)/Modules -I$(OSHOME)/PW -I$(OSHOME)/PH # # Fortran compiler: # # F90 = sxmpif90 F77 = sxmpif90 FFLAGS = $(BASIC) $(MISC) $(OPT) $(DEBUGOPT) #$(FTRACE) #FFLAGS = $(BASIC) $(MISC) $(DEBUG) $(DEBUGOPT) $(OPT0) #FCAUTIOUS=$(BASIC) $(MISC1) $(DEBUG) $(DEBUGOPT) F90FLAGS=$(FFLAGS) F77FLAGS=-f0 $(FFLAGS) # # C compiler: # #CC = sxc++ #CFLAGS = -DLANGUAGE_C -DNEC -DSX -I$(INC_DIR) -hfloat0,0,acct CC = sxcc CCLOCAL=cc CCFLAGS = -D__INTEL -D__LINUX64 -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA -I$(INC_DIR) # # Libraries: # # With ASL fft libraries LIBS = -llapack -lblas # With libfft (Mathkeisan) libraries # be careful, versions <= 1.4 are buggy (zzfft3d), #wait for 1.5 (expected end of 2003) #LIBS = -llapack -lblas $(OSHOME)/zzfft3d.o -lfft # You can find the jmfft Cray compatible library written # by Jean-Marie Teuler on www.idris.fr (search for jmfft) #LIBS = -llapack -lblas -L$(HOME)/mylocal/lib -ljmfft # # Loader flags: # LD = $(F90) #LDFLAGS = $(BASIC) $(PROF) $(FTRACE) LDFLAGS = $(BASIC) $(DEBUG) $(DEBUGOPT) $(OSHOME)/flib/ptools.a \ $(OSHOME)/flib/flib.a $(OSHOME)/clib/clib.a \ -p -Wl" -f zero " $(LIBS) RANLIB = echo ============================================================================= Thanks! Best regards, William On Thu, 28 Dec 2006, Axel Kohlmeyer wrote: > On 12/28/06, wlyim at puccini.che.pitt.edu wrote: > > Thanks for your suggestion. I will try one of the examples as soon as > > possible. > > > > Current status: ifort-compiled pw.x and ph.x can complete the job > > normally. However, the NEC executables pass a larger "nrxx" value, 22200 > > in NEC vs 20736 in Intel, given that nr1=24,nr2=24,nr3=36. So in NEC, some > > that is very interesting. > > > zero "zeta" were passed to dmxc_spin subroutine which led to "divide by > > zero" error at line 1192 in Modules/functionals.f90. Interestingly, pw.x > > by sxcross compiler and ifort gave the same scf results, while ph.x in NEC > > didn't work... > > no surprise here. pw.x does not need the derivatives of the exchange- > correlation potential. > > > Any suggestion is welcome, e.g. compiler options, preprocessor flags... > > from looking at the code it seems that the relation nrxx=nrx1*nrx2*nrx3 is > only true in the serial case. see Modules/fft_types.f90 lines 242ff. > > the intel compiler code usually continues with a denormalized number > (NaN or Inf) after a division by zero (same as IBM xlf) and since the > corresponding grid point is not accessed this does not propagate. > > to remedy the situation you can try a) compile a serial version of the code, > b) look for a compiler flag to continue after a denormalized number, or > c) correct the code in PH/phq_setup.f90 to call dmxc()/dmxc_spin() > only for values or 'ir' that correspond to valid grid points. > > cheers, > axel. > > > > > > Best regards, > > William > > > > > -- Dr. Wai-Leung Yim Institut fuer Reine und Angewandte Chemie, Theoretische Chemie, Carl von Ossiezky Universtaet Oldenburg, 26129 Oldenburg, Germany Email: wlyim at puccini.che.pitt.edu Phone: +49-441-798-3950 (office) +49-441-798-5102 (home) Fax: +49-441-798-3964 From akohlmey at cmm.chem.upenn.edu Fri Dec 29 17:28:13 2006 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Fri, 29 Dec 2006 11:28:13 -0500 (EST) Subject: [Pw_forum] ph.x v3.2 on NEC SX-8 In-Reply-To: Message-ID: On Fri, 29 Dec 2006 wlyim at puccini.che.pitt.edu wrote: WL> Thank Axel for fruitful discussion. WL> WL> The larger nrxx index in NEC is come from the "good_fft_dimension" WL> subroutine, and nrxx=25x24x37 (=22200), instead of 24x24x36 in INTEL. WL> I found that I cannot simply neglect the "zero" elements after I tried two WL> things: WL> 1. masked the overflow error can pass through the phq_setup step, but WL> after the whole phonon cycles, it hanged at some point; WL> 2. modified the dmxc_spin subroutine and kept the extra array zero. The WL> program can run till the end but the result was wrong. right. the unusable elements will be scattered across the array, so just setting the last block to zero will not help. i'd change the loop to only compute the derivative if there is significant density (i.e. check the rhotot or rhoup/rhodw arrays, respectively). actually, if you look at the non-spinpolarized case, this has already been implemented. it also tries to handle negative densities... WL> Till now, I cannot find a way to solve the ph.x problem in NEC (pw.x WL> works). I will be appreciated if someone will address this issue. there may be two more options that you want to try out: a) you can set the fft grid dimensions (in the pw.x input already) manually (see: Docs/INPUT_PW). i would try: nr1=25, nr2=25, nr3=37 as some comment in the NEC fft driver suggests, that it needs odd grid dimensions. b) you can try to use the internal FFT by changing DFLAGS to not contain -DASL and add -D__FFTW and -D__USE_INTERNAL_FFTW instead. (see: include/defs.h.README) 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 giannozz at nest.sns.it Sat Dec 30 23:18:16 2006 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Sat, 30 Dec 2006 23:18:16 +0100 Subject: [Pw_forum] Self-Interaction-Correction (SIC In-Reply-To: <1167034246.458f8786dc4f1@webmail.sissa.it> References: <20061224120336.59535.qmail@web15005.mail.cnb.yahoo.com> <1167034246.458f8786dc4f1@webmail.sissa.it> Message-ID: <200612302318.16070.giannozz@nest.sns.it> On Monday 25 December 2006 09:10, Xunlei Ding wrote: > When you generate PP, you can set "isic= 1" to include the SIC (see > INPUT_LD1 in $espresso/atomic_doc). I think that "isic=1" should work (using Perdew-Zunger procedure) only for atomic calculations. I don't think it is not implemented in other cases. There is - in CP only - an implementation of SIC for systems with one unpaired electron (using the procedure by Mauri et al). There has been some work to implement SIC in pseudopotentials, using Filippetti and Spaldin procedure, but it is far from a usable state. > Quoting ?????? ?? : > > Dear users, > > I need include the Self-Interaction-Correction (SIC) in the calculation, > > and i found SIC need to be included by myself, but I'm a new user of pw. > > So can you help me? i'll be appreciate your help. > > yours sincerely, > > hongxia Paolo Giannozzi