[Wien] Electronic density for a given K point.
Thank you very much Dr. Blaha. We reproduce successfully these graphs. Jos? A. Camargo Mart?nez DEPARTAMENTO DE F?SICA CINVESTAV - M?XICO D.F. De: Peter Blaha pblaha at theochem.tuwien.ac.at Para: A Mailing list for WIEN2k users wien at zeus.theochem.tuwien.ac.at Enviado: Jueves 21 de febrero de 2013 1:51 Asunto: Re: [Wien] Electronic density for a given K point. You can for instance put the coordinates of the desired k-point put into case.klist (ix,iy,iz,i-denominator), then x lapw1 examine case.output1 and find the eigenvalue you want to plot: x lapw2 -all emin emax? ? ? (where emin/emax should bracket the desired eigenvalue. If the k-point is already in klistm you may simply bracket the eigenvalue very closely, so that no other eigenvalue falls into that region. Am 21.02.2013 05:23, schrieb Jose Alfredo Camargo Martinez: Hi everyone In the plots from paper? DOI: 10.1002/qua.560230435 (P. Blaha and K. Schwarz, Int. J. Quantum Chem. 23, 1535 (1983), it was determined in which case the Ti_d-C_p bonds are either bonding or anti-bonding. In such paper the electronic density for a K point, named Delta (which is in between the Gamma and X points) was calculated, as well as for two eigen-values with Delta symmetry. How can we calculate the corresponding electronic density for a given K point? We have searched for information both in the user guide and the Mailig list. thanks in advance. Jos? A. Camargo Mart?nez DEPARTAMENTO DE F?SICA CINVESTAV - M?XICO D.F. ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- Peter Blaha Inst.Materials Chemistry TU Vienna Getreidemarkt 9 A-1060 Vienna Austria +43-1-5880115671 ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- next part -- An HTML attachment was scrubbed... URL: http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20130222/8e99c7dc/attachment.htm
[Wien] trying to install WIEN2k on Ubuntu 12.04 64-bit
Hello, I am trying to install the current version 12.1 on Ubuntu 12.04 (64-bit). I met some problem related to mpi, can someone please give me some hint?Thanks in advance. The situation is like this, on a freshly installed Ubuntu 12.04 64bit, I installed current version Intel Fortran Composer XE 2013.2.146, and installed MPICH2 and FFTW3 via Ubuntu Software Center. Before run the siteconfig_lapw, I checked which ifort /opt/intel/composer_xe_2013.2.146/bin/intel64/ifort which mpif90 /usr/bin/mpif90 and did the following 3 lines in the terminal source /opt/intel/composer_xe_2013.2.146/bin/compilervars.sh intel64 export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/intel/composer_xe_2013.2.146/mkl/lib/intel64 export MKLROOT=/opt/intel/composer_xe_2013.2.146/mkl/ Then I run the siteconfig_lapw, and selected system as ifort12+mkl (the first one), selected compilers as ifort and cc, selected finegrained parallel and mpif90, and got error message like this: --- cut1 --- Compile time errors (if any) were: SRC_hf/compile.msg:make[1]: *** [modules.o] Error 1 SRC_hf/compile.msg:make: *** [rp] Error 2 SRC_hf/compile.msg:make[1]: *** [modules.o] Error 1 SRC_hf/compile.msg:make: *** [cp] Error 2 SRC_lapw0/compile.msg:make[1]: *** [modules.o] Error 1 SRC_lapw0/compile.msg:make: *** [para] Error 2 SRC_lapw1/compile.msg:make[1]: *** [modules.o] Error 1 SRC_lapw1/compile.msg:make: *** [rp] Error 2 SRC_lapw1/compile.msg:make[1]: *** [modules.o] Error 1 SRC_lapw1/compile.msg:make: *** [cp] Error 2 SRC_lapw2/compile.msg:make[1]: *** [modules.o] Error 1 SRC_lapw2/compile.msg:make: *** [rp] Error 2 SRC_lapw2/compile.msg:make[1]: *** [modules.o] Error 1 SRC_lapw2/compile.msg:make: *** [cp] Error 2 --- cut1 --- I looked into SRC_lapw1/compile.msg, and the detailed error is: --- cut2 --- mpif90 -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -DFFTW3 -traceback -DParallel -c modules_tmp_.F -- The Open MPI wrapper compiler was unable to find the specified compiler gfortran in your PATH. Note that this compiler was either specified at configure time or in one of several possible environment variables. -- make[1]: *** [modules.o] Error 1 make[1]: Leaving directory `/home/lzhang200/wien2k/SRC_lapw1' make: *** [rp] Error 2 --- cut2 --- It seems OpenMPI was invoked and it looked for gfortran. I don't have gfortran installed at all, but I found I have openmpi installed. I then used Ubuntu Software Center to search openmpi and uninstalled related packages. I restarted the system and repeated the siteconfig_lapw. However I still get error message, not same but similar, it still looks for gfortran, for example the SRC_lapw1/compile.msg shows: --- cut3 --- mpif90 -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -DFFTW3 -traceback -DParallel -c modules_tmp_.F /usr/bin/mpif90: line 370: gfortran: command not found make[1]: *** [modules.o] Error 127 make[1]: Leaving directory `/home/lzhang200/wien2k/SRC_lapw1' make: *** [rp] Error 2 --- cut3 --- I did not specify to use gfortran anywhere in the setup of siteconfig_lapw, I don't see why mpif90 keeps looking for it. How can I fix this problem? Thanks a lot. Regards, Long Zhang -- next part -- An HTML attachment was scrubbed... URL: http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20130222/3e9c6516/attachment.htm
[Wien] Symmetso-error
Dear Prof Blaha, Thank you very much for pointing out my mistake. Yes, just replacing P by H resolves this problem. Also, replacing 120 by 120.1 can also avoid the error, but not desirable. With kind regards Prasenjit Roy Electronic Structures of Materials Radboud University Nijmegen -- next part -- An HTML attachment was scrubbed... URL: http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20130222/0b28aea9/attachment.htm
[Wien] trying to install WIEN2k on Ubuntu 12.04 64-bit
`/home/lzhang200/wien2k/SRC_lapw1' make: *** [rp] Error 2 --- cut3 --- I did not specify to use gfortran anywhere in the setup of siteconfig_lapw, I don't see why mpif90 keeps looking for it. How can I fix this problem? Thanks a lot. Regards, Long Zhang ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- next part -- An HTML attachment was scrubbed... URL: http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20130222/c8a94c3e/attachment.htm
[Wien] trying to install WIEN2k on Ubuntu 12.04 64-bit
I keep saying this all the time: The mpi-parallel version needs special hardware ! It is not of much use on a single quadcore-cpu. A cluster needs a fast network like infiniband. Only then the installation of the mpi-version make sense. We have a k-point parallel version, which does not need mpi, but is perfect for a small cluster with a common NFS filesystem. Am 22.02.2013 06:20, schrieb Long Zhang: Hello, I am trying to install the current version 12.1 on Ubuntu 12.04 (64-bit). I met some problem related to mpi, can someone please give me some hint? Thanks in advance. The situation is like this, on a freshly installed Ubuntu 12.04 64bit, I installed current version Intel Fortran Composer XE 2013.2.146, and installed MPICH2 and FFTW3 via Ubuntu Software Center. Before run the siteconfig_lapw, I checked which ifort /opt/intel/composer_xe_2013.2.146/bin/intel64/ifort which mpif90 /usr/bin/mpif90 and did the following 3 lines in the terminal source /opt/intel/composer_xe_2013.2.146/bin/compilervars.sh intel64 export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/intel/composer_xe_2013.2.146/mkl/lib/intel64 export MKLROOT=/opt/intel/composer_xe_2013.2.146/mkl/ Then I run the siteconfig_lapw, and selected system as ifort12+mkl (the first one), selected compilers as ifort and cc, selected finegrained parallel and mpif90, and got error message like this: --- cut1 --- Compile time errors (if any) were: SRC_hf/compile.msg:make[1]: *** [modules.o] Error 1 SRC_hf/compile.msg:make: *** [rp] Error 2 SRC_hf/compile.msg:make[1]: *** [modules.o] Error 1 SRC_hf/compile.msg:make: *** [cp] Error 2 SRC_lapw0/compile.msg:make[1]: *** [modules.o] Error 1 SRC_lapw0/compile.msg:make: *** [para] Error 2 SRC_lapw1/compile.msg:make[1]: *** [modules.o] Error 1 SRC_lapw1/compile.msg:make: *** [rp] Error 2 SRC_lapw1/compile.msg:make[1]: *** [modules.o] Error 1 SRC_lapw1/compile.msg:make: *** [cp] Error 2 SRC_lapw2/compile.msg:make[1]: *** [modules.o] Error 1 SRC_lapw2/compile.msg:make: *** [rp] Error 2 SRC_lapw2/compile.msg:make[1]: *** [modules.o] Error 1 SRC_lapw2/compile.msg:make: *** [cp] Error 2 --- cut1 --- I looked into SRC_lapw1/compile.msg, and the detailed error is: --- cut2 --- mpif90 -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -DFFTW3 -traceback -DParallel -c modules_tmp_.F -- The Open MPI wrapper compiler was unable to find the specified compiler gfortran in your PATH. Note that this compiler was either specified at configure time or in one of several possible environment variables. -- make[1]: *** [modules.o] Error 1 make[1]: Leaving directory `/home/lzhang200/wien2k/SRC_lapw1' make: *** [rp] Error 2 --- cut2 --- It seems OpenMPI was invoked and it looked for gfortran. I don't have gfortran installed at all, but I found I have openmpi installed. I then used Ubuntu Software Center to search openmpi and uninstalled related packages. I restarted the system and repeated the siteconfig_lapw. However I still get error message, not same but similar, it still looks for gfortran, for examplethe SRC_lapw1/compile.msg shows: --- cut3 --- mpif90 -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -DFFTW3 -traceback -DParallel -c modules_tmp_.F /usr/bin/mpif90: line 370: gfortran: command not found make[1]: *** [modules.o] Error 127 make[1]: Leaving directory `/home/lzhang200/wien2k/SRC_lapw1' make: *** [rp] Error 2 --- cut3 --- I did not specify to use gfortran anywhere in the setupof siteconfig_lapw, I don't see why mpif90 keeps looking for it. How can I fix this problem? Thanks a lot. Regards, Long Zhang ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- Peter Blaha Inst.Materials Chemistry TU Vienna Getreidemarkt 9 A-1060 Vienna Austria +43-1-5880115671
[Wien] Spin-orbit interaction
Dear Wien2k users, My name is Chikashi Suzuki, from Japan Atomic Energy Agency. I am running wien version WIEN2k 10.1. I calculate the electronic structure of americium oxides and uranium oxides. These calculations need spin-orbit interaction. I wonder if this spin-orbit interaction in Wien2k is collinear or non-collinear approximation. I could not find discriptions about it in the user's guide. Sincerely yours *** Dr. Chikashi Suzuki Research Group for Nuclear Materials Modeling Nuclear Science and Engineering Directorate Japan Atomic Energy Agency Tokai-mura, Naka-gun, Ibaraki-ken 319-1195, Japan Tel: +81-29-282-6373 Fax: +81-29-282-6122 Email: suzuki.chikashi at jaea.go.jp E-mail?suzuki.chikashi at jaea.go.jp ***
[Wien] Incomplete DOS
Dear Users, I am calculating the DOS for binary compound TaN and getting DOS only before fermi level. I increased the Emax from 1.2 to 4 Ry in case.int file. Even then I am not getting full DOS., Please help me. Regards, mamta -- next part -- An HTML attachment was scrubbed... URL: http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20130222/386041e5/attachment.htm
[Wien] Incomplete DOS
I am calculating the DOS for binary compound TaN and getting DOS only before fermi level. I increased the Emax from 1.2 to 4 Ry in case.int http://case.int file. Even then I am not getting full DOS., Please help me. You might need to increase EMAX in case.in1(c) as well. Rerun lapw1 (or rerun an entire iteration), then proceed with all the usual steps for the DOS. Stefaan
[Wien] MPI
Dear Prof. Blaha, Prof. Marks and Wien2k community, I noticed that the siteconfig_lapw defines MPI_REMOTE as setenv MPI_REMOTE 1 even when one answers 0 to the correspondent question. I had previously changed it to 0, but I believe that I recompiled something after that and the value 1 was set again. I am doing another test to check if this the origin of my problems with openmpi. Unfortunately, I am not proficient in shell scripts, so I can not point the exact problem with the MPI_REMOTE setting (even if there is a real one). Thank you one more time for the help, Luis Ogando 2013/2/20 Peter Blaha pblaha at theochem.tuwien.ac.at On an SMP machine make sure you have in $WIENROOT/parallel_options setenv USE_REMOTE 0 setenv MPI_REMOTE 0 Am 20.02.2013 17:45, schrieb Luis Ogando: Dear Prof. Marks, Thank you very much for your prompt answer. I am using openmpi, but I believe that I am facing some of the tricky issues you mentioned. I work in a SMP machine and the calculation starts fine. After some tens of iterations, MPI suddenly asks for a password and everything goes down to the drain. I am using open mpi 1.6. Do you recommend any older version ?? All the best, Luis Ogando 2013/2/20 Laurence Marks L-marks at northwestern.edu mailto:L-marks at northwestern.**edu L-marks at northwestern.edu One that works. Some versions of openmpi have problems although that is probably the best option for the future. There are some tricky issues with openmpi related to how your flavor of ssh works, there is no standard and some do not propogate kill commands which means that they can leave orphans. An alternative is mvapich. In a benchmark that I did a few months ago the Intel mpi was much better for AVX instructions, but that may have changed. Openmpi is easy to compile; mvapich can be a little trickier. N.B., if you have fast connections, e.g. infiniband, they are more than fast enough and I have never seen this as rate limiting with Wien2k. With ethernet it matters. On Wed, Feb 20, 2013 at 10:29 AM, Luis Ogando lcodacal at gmail.com mailto:lcodacal at gmail.com wrote: Dear Wien2k community, Is there any recommended flavor and version of an MPI compiler to use with Intel(R) Fortran Intel(R) 64 Compiler XE for applications running on Intel(R) 64, Version 12.0.3.174 Build 20110309 ? All the best, Luis Ogando -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu http://www.numis.**northwestern.eduhttp://www.numis.northwestern.edu 1-847-491-3996 tel:1-847-491-3996 Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-Gyorgi __**_ Wien mailing list Wien at zeus.theochem.tuwien.ac.**at Wien at zeus.theochem.tuwien.ac.atmailto: Wien at zeus.theochem.**tuwien.ac.at Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.**ac.at/mailman/listinfo/wienhttp://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien __**_ Wien mailing list Wien at zeus.theochem.tuwien.ac.**at Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.**ac.at/mailman/listinfo/wienhttp://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- Peter Blaha Inst.Materials Chemistry TU Vienna Getreidemarkt 9 A-1060 Vienna Austria +43-1-5880115671 __**_ Wien mailing list Wien at zeus.theochem.tuwien.ac.**at Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.**ac.at/mailman/listinfo/wienhttp://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- next part -- An HTML attachment was scrubbed... URL: http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20130222/890e8291/attachment.htm
[Wien] MPI
.**ac.at/mailman/listinfo/wienhttp://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien __**_ Wien mailing list Wien at zeus.theochem.tuwien.ac.**at Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.**ac.at/mailman/listinfo/wienhttp://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- Peter Blaha Inst.Materials Chemistry TU Vienna Getreidemarkt 9 A-1060 Vienna Austria +43-1-5880115671 __**_ Wien mailing list Wien at zeus.theochem.tuwien.ac.**at Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.**ac.at/mailman/listinfo/wienhttp://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- next part -- An HTML attachment was scrubbed... URL: http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20130222/7292d9bc/attachment.htm
[Wien] Syntax error in array constructor (gfortran)
Dear Gavin, thank you for your reply. I agree and it might work well. but, I think it would be more favorable if source compatibility is kept in different compilers. Anyway, thanks again for your comments. With best regards, Tomo - Original Message - I think you have to modify the code like you indicated. I made the attached patch. It removed the compile time errors, but I never tested it make sure it didn't have any runtime errors. Placed gfortran.patch (for Wien2k 12.1) into $WIENROOT, and entered: $ patch -b -p0 -i gfortran.patch On 2/20/2013 11:26 PM, tasaka at affinity-science.com wrote: Hello, I encountered the follwoing errors when compiling in SRC_hf with GNU Fortran (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3. if there are any options of gfortran to avoid these errors, please advise. // gfortran -ffree-form -O2 -ffree-line-length-none -c calc_exhfvv_tmp_.F calc_exhfvv_tmp_.F:269.22: igv = (/ 1:ng /) 1 Error: Syntax error in array constructor at (1) calc_exhfvv_tmp_.F:272.22: igv = (/ 1:(igs-1),(igs+1):ng /) 1 Error: Syntax error in array constructor at (1) make[1]: *** [calc_exhfvv.o] Error 1 // Or, should I modify the codes as like below? igv = (/ (i, i=1,ng,1) /) Any information would be appreciated. With best regards, Tomo ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
[Wien] trying to install WIEN2k on Ubuntu 12.04 64-bit
__**_ Wien mailing list Wien at zeus.theochem.tuwien.ac.**at Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.**ac.at/mailman/listinfo/wienhttp://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- Peter Blaha Inst.Materials Chemistry TU Vienna Getreidemarkt 9 A-1060 Vienna Austria +43-1-5880115671 __**_ Wien mailing list Wien at zeus.theochem.tuwien.ac.**at Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.**ac.at/mailman/listinfo/wienhttp://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- next part -- An HTML attachment was scrubbed... URL: http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20130222/d21eb493/attachment.htm
[Wien] trying to install WIEN2k on Ubuntu 12.04 64-bit
As Peter said, the simplest approach is just k-point parallel which does not need OpenMP. The rate limiting steps are lapack calls which the Intel mkl is good for. Whether mpi is good for a small cluster such as you have in not so clear. Peter has benchmarked the mpi version and his conclusion is that it is not useful; I have benchmarked on my cluster and I have consistently found the mpi versions to be faster than the Intel threading. I suspect that it really depends upon many details specific to the systems, for instance cross-core optimizations, network and memory speed Not a complete answer, but for certain the simplest approach is to just use k-point parallel. On Fri, Feb 22, 2013 at 9:55 AM, Long Zhang lzhang6789 at gmail.com wrote: That's true I agree. If the k-point parallel version does not need mpi, then it's OpenMP I suppose (please correct me if it's not). But I really don't want to run OpenMP because it will mess my other applications up. I am building it on a small server of 2 Opteron 12-core cpus. It's just a dual-cpu system, not a cluster. I am not sure if I can gain enough speed-up by using 24 cores. Anyway if I want a little k-point parallel, can I choice to use mpi? or there is no such choice at all? Thank you very much. Long On Fri, Feb 22, 2013 at 3:07 AM, Peter Blaha pblaha at theochem.tuwien.ac.at wrote: I keep saying this all the time: The mpi-parallel version needs special hardware ! It is not of much use on a single quadcore-cpu. A cluster needs a fast network like infiniband. Only then the installation of the mpi-version make sense. We have a k-point parallel version, which does not need mpi, but is perfect for a small cluster with a common NFS filesystem. Am 22.02.2013 06:20, schrieb Long Zhang: Hello, I am trying to install the current version 12.1 on Ubuntu 12.04 (64-bit). I met some problem related to mpi, can someone please give me some hint? Thanks in advance. The situation is like this, on a freshly installed Ubuntu 12.04 64bit, I installed current version Intel Fortran Composer XE 2013.2.146, and installed MPICH2 and FFTW3 via Ubuntu Software Center. Before run the siteconfig_lapw, I checked which ifort /opt/intel/composer_xe_2013.2.146/bin/intel64/ifort which mpif90 /usr/bin/mpif90 and did the following 3 lines in the terminal source /opt/intel/composer_xe_2013.2.146/bin/compilervars.sh intel64 export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/intel/composer_xe_2013.2.146/mkl/lib/intel64 export MKLROOT=/opt/intel/composer_xe_2013.2.146/mkl/ Then I run the siteconfig_lapw, and selected system as ifort12+mkl (the first one), selected compilers as ifort and cc, selected finegrained parallel and mpif90, and got error message like this: --- cut1 --- Compile time errors (if any) were: SRC_hf/compile.msg:make[1]: *** [modules.o] Error 1 SRC_hf/compile.msg:make: *** [rp] Error 2 SRC_hf/compile.msg:make[1]: *** [modules.o] Error 1 SRC_hf/compile.msg:make: *** [cp] Error 2 SRC_lapw0/compile.msg:make[1]: *** [modules.o] Error 1 SRC_lapw0/compile.msg:make: *** [para] Error 2 SRC_lapw1/compile.msg:make[1]: *** [modules.o] Error 1 SRC_lapw1/compile.msg:make: *** [rp] Error 2 SRC_lapw1/compile.msg:make[1]: *** [modules.o] Error 1 SRC_lapw1/compile.msg:make: *** [cp] Error 2 SRC_lapw2/compile.msg:make[1]: *** [modules.o] Error 1 SRC_lapw2/compile.msg:make: *** [rp] Error 2 SRC_lapw2/compile.msg:make[1]: *** [modules.o] Error 1 SRC_lapw2/compile.msg:make: *** [cp] Error 2 --- cut1 --- I looked into SRC_lapw1/compile.msg, and the detailed error is: --- cut2 --- mpif90 -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -DFFTW3 -traceback -DParallel -c modules_tmp_.F -- The Open MPI wrapper compiler was unable to find the specified compiler gfortran in your PATH. Note that this compiler was either specified at configure time or in one of several possible environment variables. -- make[1]: *** [modules.o] Error 1 make[1]: Leaving directory `/home/lzhang200/wien2k/SRC_lapw1' make: *** [rp] Error 2 --- cut2 --- It seems OpenMPI was invoked and it looked for gfortran. I don't have gfortran installed at all, but I found I have openmpi installed. I then used Ubuntu Software Center to search openmpi and uninstalled related packages. I restarted the system and repeated the siteconfig_lapw. However I still get error message, not same but similar, it still looks for gfortran, for examplethe
[Wien] trying to install WIEN2k on Ubuntu 12.04 64-bit
: *** [rp] Error 2 --- cut2 --- It seems OpenMPI was invoked and it looked for gfortran. I don't have gfortran installed at all, but I found I have openmpi installed. I then used Ubuntu Software Center to search openmpi and uninstalled related packages. I restarted the system and repeated the siteconfig_lapw. However I still get error message, not same but similar, it still looks for gfortran, for examplethe SRC_lapw1/compile.msg shows: --- cut3 --- mpif90 -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -DFFTW3 -traceback -DParallel -c modules_tmp_.F /usr/bin/mpif90: line 370: gfortran: command not found make[1]: *** [modules.o] Error 127 make[1]: Leaving directory `/home/lzhang200/wien2k/SRC_lapw1' make: *** [rp] Error 2 --- cut3 --- I did not specify to use gfortran anywhere in the setupof siteconfig_lapw, I don't see why mpif90 keeps looking for it. How can I fix this problem? Thanks a lot. Regards, Long Zhang ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- Peter Blaha Inst.Materials Chemistry TU Vienna Getreidemarkt 9 A-1060 Vienna Austria +43-1-5880115671 ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu 1-847-491-3996 Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-Gyorgi ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- next part -- An HTML attachment was scrubbed... URL: http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20130222/a8d75c38/attachment-0001.htm
[Wien] trying to install WIEN2k on Ubuntu 12.04 64-bit
. -- make[1]: *** [modules.o] Error 1 make[1]: Leaving directory `/home/lzhang200/wien2k/SRC_lapw1' make: *** [rp] Error 2 --- cut2 --- It seems OpenMPI was invoked and it looked for gfortran. I don't have gfortran installed at all, but I found I have openmpi installed. I then used Ubuntu Software Center to search openmpi and uninstalled related packages. I restarted the system and repeated the siteconfig_lapw. However I still get error message, not same but similar, it still looks for gfortran, for examplethe SRC_lapw1/compile.msg shows: --- cut3 --- mpif90 -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -DFFTW3 -traceback -DParallel -c modules_tmp_.F /usr/bin/mpif90: line 370: gfortran: command not found make[1]: *** [modules.o] Error 127 make[1]: Leaving directory `/home/lzhang200/wien2k/SRC_lapw1' make: *** [rp] Error 2 --- cut3 --- I did not specify to use gfortran anywhere in the setupof siteconfig_lapw, I don't see why mpif90 keeps looking for it. How can I fix this problem? Thanks a lot. Regards, Long Zhang ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- Peter Blaha Inst.Materials Chemistry TU Vienna Getreidemarkt 9 A-1060 Vienna Austria +43-1-5880115671 ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu 1-847-491-3996 Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-Gyorgi ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu 1-847-491-3996 Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-Gyorgi -- next part -- An HTML attachment was scrubbed... URL: http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20130222/3af447b2/attachment.htm
[Wien] trying to install WIEN2k on Ubuntu 12.04 64-bit
No. Please read the UG about parallelization. k-point parallelization is done via scripts. Am 22.02.2013 20:28, schrieb Long Zhang: Thank you for the information. I think I had wrong idea about k-point parallel. If it doesn't use OpenMP then it's perfectly fine for me. I'll drop the idea of finegrained parallel in this installation. Just want to confirm, for using k-point parallel only, MPICH2 is still required, is that right? Thanks. Long On Fri, Feb 22, 2013 at 11:04 AM, Laurence Marks L-marks at northwestern.edu mailto:L-marks at northwestern.edu wrote: As Peter said, the simplest approach is just k-point parallel which does not need OpenMP. The rate limiting steps are lapack calls which the Intel mkl is good for. Whether mpi is good for a small cluster such as you have in not so clear. Peter has benchmarked the mpi version and his conclusion is that it is not useful; I have benchmarked on my cluster and I have consistently found the mpi versions to be faster than the Intel threading. I suspect that it really depends upon many details specific to the systems, for instance cross-core optimizations, network and memory speed Not a complete answer, but for certain the simplest approach is to just use k-point parallel. On Fri, Feb 22, 2013 at 9:55 AM, Long Zhang lzhang6789 at gmail.com mailto:lzhang6789 at gmail.com wrote: That's true I agree. If the k-point parallel version does not need mpi, then it's OpenMP I suppose (please correct me if it's not). But I really don't want to run OpenMP because it will mess my other applications up. I am building it on a small server of 2 Opteron 12-core cpus. It's just a dual-cpu system, not a cluster. I am not sure if I can gain enough speed-up by using 24 cores. Anyway if I want a little k-point parallel, can I choice to use mpi? or there is no such choice at all? Thank you very much. Long On Fri, Feb 22, 2013 at 3:07 AM, Peter Blaha pblaha at theochem.tuwien.ac.at mailto:pblaha at theochem.tuwien.ac.at wrote: I keep saying this all the time: The mpi-parallel version needs special hardware ! It is not of much use on a single quadcore-cpu. A cluster needs a fast network like infiniband. Only then the installation of the mpi-version make sense. We have a k-point parallel version, which does not need mpi, but is perfect for a small cluster with a common NFS filesystem. Am 22.02.2013 06:20, schrieb Long Zhang: Hello, I am trying to install the current version 12.1 on Ubuntu 12.04 (64-bit). I met some problem related to mpi, can someone please give me some hint? Thanks in advance. The situation is like this, on a freshly installed Ubuntu 12.04 64bit, I installed current version Intel Fortran Composer XE 2013.2.146, and installed MPICH2 and FFTW3 via Ubuntu Software Center. Before run the siteconfig_lapw, I checked which ifort /opt/intel/composer_xe_2013.2.146/bin/intel64/ifort which mpif90 /usr/bin/mpif90 and did the following 3 lines in the terminal source /opt/intel/composer_xe_2013.2.146/bin/compilervars.sh intel64 export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/intel/composer_xe_2013.2.146/mkl/lib/intel64 export MKLROOT=/opt/intel/composer_xe_2013.2.146/mkl/ Then I run the siteconfig_lapw, and selected system as ifort12+mkl (the first one), selected compilers as ifort and cc, selected finegrained parallel and mpif90, and got error message like this: --- cut1 --- Compile time errors (if any) were: SRC_hf/compile.msg:make[1]: *** [modules.o] Error 1 SRC_hf/compile.msg:make: *** [rp] Error 2 SRC_hf/compile.msg:make[1]: *** [modules.o] Error 1 SRC_hf/compile.msg:make: *** [cp] Error 2 SRC_lapw0/compile.msg:make[1]: *** [modules.o] Error 1 SRC_lapw0/compile.msg:make: *** [para] Error 2 SRC_lapw1/compile.msg:make[1]: *** [modules.o] Error 1 SRC_lapw1/compile.msg:make: *** [rp] Error 2 SRC_lapw1/compile.msg:make[1]: *** [modules.o] Error 1 SRC_lapw1/compile.msg:make: *** [cp] Error 2 SRC_lapw2/compile.msg:make[1]: *** [modules.o] Error 1 SRC_lapw2/compile.msg:make: *** [rp] Error 2 SRC_lapw2/compile.msg:make[1]: *** [modules.o] Error 1 SRC_lapw2/compile.msg:make: *** [cp] Error 2 --- cut1 --- I
[Wien] Spin-orbit interaction
In standard Wien2k this is collinear. However, we also have a noncollinear version WIENNCM (see www.wien2k.at; reg_user section) Am 22.02.2013 11:33, schrieb Chikashi Suzuki (): Dear Wien2k users, My name is Chikashi Suzuki, from Japan Atomic Energy Agency. I am running wien version WIEN2k 10.1. I calculate the electronic structure of americium oxides and uranium oxides. These calculations need spin-orbit interaction. I wonder if this spin-orbit interaction in Wien2k is collinear or non-collinear approximation. I could not find discriptions about it in the user's guide. Sincerely yours *** Dr. Chikashi Suzuki Research Group for Nuclear Materials Modeling Nuclear Science and Engineering Directorate Japan Atomic Energy Agency Tokai-mura, Naka-gun, Ibaraki-ken 319-1195, Japan Tel: +81-29-282-6373 Fax: +81-29-282-6122 Email: suzuki.chikashi at jaea.go.jp E-mail?suzuki.chikashi at jaea.go.jp *** ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- Peter Blaha Inst.Materials Chemistry TU Vienna Getreidemarkt 9 A-1060 Vienna Austria +43-1-5880115671
[Wien] trying to install WIEN2k on Ubuntu 12.04 64-bit
--- I looked into SRC_lapw1/compile.msg, and the detailed error is: --- cut2 --- mpif90 -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -DFFTW3 -traceback -DParallel -c modules_tmp_.F -- The Open MPI wrapper compiler was unable to find the specified compiler gfortran in your PATH. Note that this compiler was either specified at configure time or in one of several possible environment variables. -- make[1]: *** [modules.o] Error 1 make[1]: Leaving directory `/home/lzhang200/wien2k/SRC_lapw1' make: *** [rp] Error 2 --- cut2 --- It seems OpenMPI was invoked and it looked for gfortran. I don't have gfortran installed at all, but I found I have openmpi installed. I then used Ubuntu Software Center to search openmpi and uninstalled related packages. I restarted the system and repeated the siteconfig_lapw. However I still get error message, not same but similar, it still looks for gfortran, for examplethe SRC_lapw1/compile.msg shows: --- cut3 --- mpif90 -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -DFFTW3 -traceback -DParallel -c modules_tmp_.F /usr/bin/mpif90: line 370: gfortran: command not found make[1]: *** [modules.o] Error 127 make[1]: Leaving directory `/home/lzhang200/wien2k/SRC_lapw1' make: *** [rp] Error 2 --- cut3 --- I did not specify to use gfortran anywhere in the setupof siteconfig_lapw, I don't see why mpif90 keeps looking for it. How can I fix this problem? Thanks a lot. Regards, Long Zhang ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- Peter Blaha Inst.Materials Chemistry TU Vienna Getreidemarkt 9 A-1060 Vienna Austria +43-1-5880115671 ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu 1-847-491-3996 Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-Gyorgi ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu 1-847-491-3996 Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-Gyorgi ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- next part -- An HTML attachment was scrubbed... URL: http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20130222/e987fe47/attachment.htm
[Wien] trying to install WIEN2k on Ubuntu 12.04 64-bit
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[Wien] Bader analysis
Dear Hefei, you can check the Born effective charge, which is defined as a change in polarization as a result of a small displacement of individual atoms. If this is what you would like to calculate, please check the following tutorial: https://github.com/spichardo/BerryPI/tree/master/tutorials/tutorial2 Thank you Oleg -- Oleg Rubel, PhD Scientist, Thunder Bay Regional Research Institute Adjunct Professor, Dept Physics, Lakehead University 290 Munro St, Thunder Bay, P7A 7T1, Ontario, Canada Phone: +1-807-7663350 Fax: +1-807-3441948 E-mail: orubel at lakeheadu.ca Homepage: http://www.tbrri.com/~orubel/ On 2/11/2013 at 12:13 PM, in message CAHJQQ_-ENTh34kEGJomg693ke7b8cqS0wg1Zq-SsVbusKhBw1w at mail.gmail.com, Hefei Hu huhefei at gmail.com wrote: Dear Wien2k users, I am using aim to analyze charges of atoms in unit cell. The system I am looking at is FeTe with formal charge 2+ for Fe and 2- for Te. The keyword in case.inaim I used is Surf, and below is the last several lines of output file case.outputaim for Fe. Error analysis, values in degrees RMS Angular Error 3.23050888 Sum of moduli 0.383514 Gradient weighted Error0.14598727 Rho weighted 0.153686 Estimated Charge Error 0.00056477 Electrons (only a rough estimate!) Integrated interstial charges: :RHO from Cubic Spline1.72204544 :RHO from Parabolic 1.72204461 :RHOINTE (Quadrature) 1.72204615 :VOLUME92.472093 :PARABOLIC for IND-ATOM 1 Z= 26.0 CHARGE: 25.88405837 0.11594163 :CUBESPLINE for IND-ATOM 1 Z= 26.0 CHARGE: 25.88405920 0.11594080 :RHOTOT for IND-ATOM 1 Z= 26.0 CHARGE: 25.88405992 0.11594008 total cputime: 1586.220 Wall1613.10326910019 Does this result mean that the charge of Fe is 0.12? That is far from 2+. How do I deal with interstitial charges of 1.72? I saw an old message in the maillist stated that there should be no interstitial charge in aim analysis. I am new to this aim, so any suggests are welcome. Thanks in advance! Best, Hefei ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
