Re: [Wien] crystal field splitting
Dear professor Vñictor Luaña: Thanks very much for your kindly reply. Your reply is really helpful and I will go on studying in this field. Thanks again. Sincerely Wangwei Lan From: wien-boun...@zeus.theochem.tuwien.ac.at wien-boun...@zeus.theochem.tuwien.ac.at on behalf of Víctor Luaña Cabal vic...@fluor.quimica.uniovi.es Sent: Sunday, August 23, 2015 15:37 To: A Mailing list for WIEN2k users Cc: Victor Luaña Subject: Re: [Wien] crystal field splitting On Sun, Aug 23, 2015 at 07:51:33PM +, Lan, Wangwei wrote: Dear Wien2k user: I am very new in WIEN2k. Now I am running case on our crystal system which contains a transition metal Cr. I am particularly interested in the d orbital splitting, the energy levels of 5 d orbitals. Does anyone know how to calculate the orbital splitting using WIEN2k? Wangwei, The answer is not simple and there can be more than one opinion living around. Let me express mu 0.02 euros. Crystal field splitting parameters (delta-D, i.e. t2g-eg splitting, Racah parameters, etc) is by fitting a model to the theoretical or experimental true calculations of total energy diferences between correlated electronic states. In other terms, there are no such a thing as orbital splitting as a well defined element. The orbital approach is a interpretative description, not a physical definition. There are decades that I not contribute to this old subject and I reccomend you to follow the more recent papers by Profs. Luis Seijo and Zoila Barandiarán, from the UAM (Universidad Aotónoma de Madrid). You will find in their work a good description of old and modern treatments, laike MOLCAS calculations, relativity contributions, and the huge importance of large correlation treatments. Both contribute to the development of MOLCAS. http://www.uam.es/personal_pdi/ciencias/lseijo/ http://www.uam.es/personal_pdi/ciencias/yara/ Notice that the field emerged from dealing with impurities within crystals, so most of the evolution that I learned was releted to the moleculartreatment of embedded impurities neighborhoods. On a solid state perspective, and your mention of wannier functions lets me thing you may prefer that, notice that d-d, d-s and d-p transitions correspond to heavily correlated problems, and the wave funcion perspective has a much longer tradition than TD-DFT ones, but let me just say that I know less abiout them. The conferences by Stefano Baroni on the calculation of the color of natural dies are simple awesome. http://stefano.baroni.me/presentations.html Best regards and good luck if you come new to this field, Dr. Vñictor Luaña -- . .In science a person can be convinced by a good argument. / `' \ That is almost impossible in politics or religion /(o)(o)\ (Adapted from Carl Sagan) /`. \/ .'\ Lo mediocre es peor que lo bueno, pero también es peor / '`'` \ que lo malo, porque la mediocridad no es un grado, es una | \'`'`/ | actitud -- Jorge Wasenberg, 2015 | |'`'`| | (Mediocre is worse than good, but it is also worse than \/`'`'`'\/ bad, because mediocrity is not a grade, it is an attitude) ===(((==)))==+= ! Dr.Víctor Luaña, in silico chemist prof. ! I hate the bureaucracy ! Departamento de Química Física y Analítica ! imposed by companies to ! Universidad de Oviedo, 33006-Oviedo, Spain ! which I owe nothing: ! e-mail: vic...@fluor.quimica.uniovi.es ! amazon, ResearchGATE and ! phone: +34-985-103491 fax: +34-985-103125 ! the like. ++ GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] 'libfftw3_mpi.so.3' is not found
Dear Prof. Lyudmila Dobysheva
thanks for your quick response. In cross checked my .bashrc file and this
was properly written. I am pasting all my .bashrc content here. Kindly,
verify them.
==
#adding mkl en. variable
source /opt/intel/composerxe-2011.3.174/bin/compilervars.sh intel64
source /opt/intel/composerxe-2011.3.174/mkl/bin/mklvars.sh intel64
source /opt/intel/impi/5.1.0.079/bin64/mpivars.sh intel64
export MKL_TARGET_ARCH=intel64
#
PATH=/opt/intel/composerxe-2011.3.174/bin/intel64:${PATH}
#PATH=/opt/intel/composerxe-2011.3.174/mkl/bin/mklvars.sh:${PATH}
PATH=/usr/local/bin:${PATH}
export PATH
#
MANPATH=/opt/intel/composerxe-2011.3.174//man:${MANPATH}
export MANPATH
#
LD_LIBRARY_PATH=/opt/intel/composerxe-2011.3.174/compiler/lib/intel64:${LD_LIBRARY_PATH}
LD_LIBRARY_PATH=/opt/intel/composerxe-2011.3.174/mkl/lib/intel64:${LD_LIBRARY_PATH}
LD_LIBRARY_PATH=/usr/local/lib:${LD_LIBRARY_PATH}
LD_LIBRARY_PATH=/home/shuvra/fftw334/lib:${LD_LIBRARY_PATH}
export LD_LIBRARY_PATH
#
INCLUDE=/opt/intel/composerxe-2011.3.174/compiler/include:${INCLUDE}
INCLUDE=/opt/intel/composerxe-2011.3.174/mkl/include:${INCLUDE}
export INCLUDE
#
MKLROOT=/opt/intel/composerxe-2011.3.174/mkl/bin/mklvars.sh:${PATH}
export MKLROOT
#
INTEL_LICENSE_FILE=/opt/intel/licenses
export INTEL_LICENSE_FILE
#export PATH:$PATH:/usr/local/bin
#export LD_LIBRARY_PATH:$LD_LIBRARY_PATH:/usr/local/lib
export OMPI_FC='ifort'
export OMPI_F77='ifort'
export OMPI_CC='icc
==
Kindly, cross check
thanks for your help
Regards,
venkatesh
___
Wien mailing list
Wien@zeus.theochem.tuwien.ac.at
http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
SEARCH the MAILING-LIST at:
http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] 'libfftw3_mpi.so.3' is not found
24.08.2015 08:47, venkatesh chandragiri wrote: I am getting error while running lapw0_mpi (in volume optimization process). These errors are /opt/intel/composerxe-2011.3.174/mkl/bin/mklvars.sh/hup http://mklvars.sh/hup: Not a directory. First, the system complains about non-existing directory, all other errors are due to the absent way. My .bashrc gives a path to fortran setting: source /opt/intel/composer_xe_2011_sp1.7.256/bin/compilervars.sh intel64 Inside this file compilervars.sh, there is a line: if [ -e $PROD_DIR/mkl/bin/mklvars.sh ]; then . $PROD_DIR/mkl/bin/mklvars.sh $1 $2 So, your fortran setting and this line form wrongly the path to non-existing directory: /opt/intel/composerxe-2011.3.174/mkl/bin/mklvars.sh/hup Maybe it should be /opt/intel/composerxe-2011.3.174/mkl/bin/mklvars.sh Or an additional suffix (intel64 in my case, after a space) Find the place where your fortran is set and check the directory Best wishes Lyudmila Dobysheva -- Phys.-Techn. Institute of Ural Br. of Russian Ac. of Sci. 426001 Izhevsk, ul.Kirova 132 RUSSIA -- Tel.:7(3412) 432045(office), 722529(Fax) E-mail: l...@ftiudm.ru, lyuk...@mail.ru (office) lyuk...@gmail.com (home) Skype: lyuka17 (home), lyuka18 (office) http://ftiudm.ru/content/view/25/103/lang,english/ -- ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] 'libfftw3_mpi.so.3' is not found
24.08.2015 11:02, venkatesh chandragiri пишет: I am pasting all my .bashrc content here. I do not see anything bad in it. 1) make set aaa and check all paths in the file aaa if they are correct. 2) Just for a case: if you send jobs through a controlling file in a batch mode, then make the same (set aaa and check) through a batch mode (sometimes pathes are transfered to a shell in a different way). 3) I am not an expert in mpi calculations, but the system definitely tells you about a wrong path: These errors are /opt/intel/composerxe-2011.3.174/mkl/bin/mklvars.sh/hup http://mklvars.sh/hup: Not a directory. Seek for this place. Where this hup and http has appeared from? Best wishes Lyudmila Dobysheva -- Phys.-Techn. Institute of Ural Br. of Russian Ac. of Sci. 426001 Izhevsk, ul.Kirova 132 RUSSIA -- Tel.:7(3412) 432045(office), 722529(Fax) E-mail: l...@ftiudm.ru, lyuk...@mail.ru (office) lyuk...@gmail.com (home) Skype: lyuka17 (home), lyuka18 (office) http://ftiudm.ru/content/view/25/103/lang,english/ -- ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] 'libfftw3_mpi.so.3' is not found
As the error states, on one or more of the computers the path to the fftw3 library is not known. This is a standard problem in openmpi. It does not fully export your environment for you, so just because the path and shared libraries are found when you source the compiler scripts does not mean they are when the program executes. Check your LD_LIBRARY_PATH edit parallel_options such that WIEN_MPIRUN exports it for you, looking at the MPIRUN man page (e.g. https://www.open-mpi.org/doc/v1.8/man1/mpirun.1.php). Alternatively use status linking for the fftw3 libraries. --- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University http://www.numis.northwestern.edu Corrosion in 4D http://MURI4D.numis.northwestern.edu Co-Editor, Acta Cryst A Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-Gyorgi On Aug 24, 2015 00:48, venkatesh chandragiri venkyphysicsi...@gmail.com wrote: Dear Wien2k users, Recently, I have installed Wien2K_13.1 program in my SMP, having 12 threads. I have run serial calculations without giving an error with this PC. Now, I want to implement parallel calculations and installed 'fftw-3.3.4', 'l_mpi_p_5.1.0.038' and 'openmpi-1.8.8'. Although, the re-installation of Wien2k with parallel option does not give any errors, I am getting error while running lapw0_mpi (in volume optimization process). These errors are === clmextrapol_lapw has generated a new Gd3Mn2vol.clmdn /opt/intel/composerxe-2011.3.174/mkl/bin/mklvars.sh/hup: Not a directory. /home/shuvra/wien2k/lapw0_mpi: error while loading shared libraries: libfftw3_mpi.so.3: cannot open shared object file: No such file or directory /home/shuvra/wien2k/lapw0_mpi: error while loading shared libraries: libfftw3_mpi.so.3: cannot open shared object file: No such file or directory /home/shuvra/wien2k/lapw0_mpi: error while loading shared libraries: libfftw3_mpi.so.3: cannot open shared object file: No such file or directory /home/shuvra/wien2k/lapw0_mpi: error while loading shared libraries: libfftw3_mpi.so.3: cannot open shared object file: No such file or directory /home/shuvra/wien2k/lapw0_mpi: error while loading shared libraries: libfftw3_mpi.so.3: cannot open shared object file: No such file or directory stop error ERROR status in Gd3Mn2vol_vol__-8.0 = However, libfftw3_mpi.so.3 file is present the in the respective path and wien2k unable to locate it..? these are the setting of the parallelization = Current settings: FFTW_LIB + FFTW_OPT : -lfftw3_mpi -lfftw3 -L/home/shuvra/fftw334/lib + -DFFTW3 -I/home/shuvra/fftw334/include (already set) RP RP_LIB(SCALAPACK+PBLAS): -lmkl_scalapack_lp64 -lmkl_solver_lp64 -lmkl_blacs_lp64 $(R_LIBS) FP FPOPT(par.comp.options): -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback MP MPIRUN commando : mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_ = Kindly, help me thanking you Best regards, venkatesh ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] 'libfftw3_mpi.so.3' is not found
Static (not status) -- Android autocorrect error. --- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University http://www.numis.northwestern.edu Corrosion in 4D http://MURI4D.numis.northwestern.edu Co-Editor, Acta Cryst A Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-Gyorgi On Aug 24, 2015 06:19, Laurence Marks l-ma...@northwestern.edu wrote: As the error states, on one or more of the computers the path to the fftw3 library is not known. This is a standard problem in openmpi. It does not fully export your environment for you, so just because the path and shared libraries are found when you source the compiler scripts does not mean they are when the program executes. Check your LD_LIBRARY_PATH edit parallel_options such that WIEN_MPIRUN exports it for you, looking at the MPIRUN man page (e.g. https://www.open-mpi.org/doc/v1.8/man1/mpirun.1.php). Alternatively use status linking for the fftw3 libraries. --- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University http://www.numis.northwestern.edu Corrosion in 4D http://MURI4D.numis.northwestern.edu Co-Editor, Acta Cryst A Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-Gyorgi On Aug 24, 2015 00:48, venkatesh chandragiri venkyphysicsi...@gmail.com wrote: Dear Wien2k users, Recently, I have installed Wien2K_13.1 program in my SMP, having 12 threads. I have run serial calculations without giving an error with this PC. Now, I want to implement parallel calculations and installed 'fftw-3.3.4', 'l_mpi_p_5.1.0.038' and 'openmpi-1.8.8'. Although, the re-installation of Wien2k with parallel option does not give any errors, I am getting error while running lapw0_mpi (in volume optimization process). These errors are === clmextrapol_lapw has generated a new Gd3Mn2vol.clmdn /opt/intel/composerxe-2011.3.174/mkl/bin/mklvars.sh/hup: Not a directory. /home/shuvra/wien2k/lapw0_mpi: error while loading shared libraries: libfftw3_mpi.so.3: cannot open shared object file: No such file or directory /home/shuvra/wien2k/lapw0_mpi: error while loading shared libraries: libfftw3_mpi.so.3: cannot open shared object file: No such file or directory /home/shuvra/wien2k/lapw0_mpi: error while loading shared libraries: libfftw3_mpi.so.3: cannot open shared object file: No such file or directory /home/shuvra/wien2k/lapw0_mpi: error while loading shared libraries: libfftw3_mpi.so.3: cannot open shared object file: No such file or directory /home/shuvra/wien2k/lapw0_mpi: error while loading shared libraries: libfftw3_mpi.so.3: cannot open shared object file: No such file or directory stop error ERROR status in Gd3Mn2vol_vol__-8.0 = However, libfftw3_mpi.so.3 file is present the in the respective path and wien2k unable to locate it..? these are the setting of the parallelization = Current settings: FFTW_LIB + FFTW_OPT : -lfftw3_mpi -lfftw3 -L/home/shuvra/fftw334/lib + -DFFTW3 -I/home/shuvra/fftw334/include (already set) RP RP_LIB(SCALAPACK+PBLAS): -lmkl_scalapack_lp64 -lmkl_solver_lp64 -lmkl_blacs_lp64 $(R_LIBS) FP FPOPT(par.comp.options): -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback MP MPIRUN commando : mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_ = Kindly, help me thanking you Best regards, venkatesh ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Control of very small fraction of atoms in alloy
Dear Lyudmila, Thank you for your e-mail with kind explanation. Sorry for having forgotten to answer earlier but it seems that the task is going well now on the belief that the first guess on simulation direction is right by your supporting advice , and with the tips you provided. We made a large supercell first and then put one of two atoms forcefully and manually, which looks a possible solution for now. So far so good. :-) I'll keep the number of parameters in mind so that they are not making too heavy loads on the simulation computer. Thank you so much and good luck with your works! - Sincerely, Seongjae. - Original Message - From: Lyudmila Dobysheva lyuk...@mail.ru To: A Mailing list for WIEN2k users wien@zeus.theochem.tuwien.ac.at Date: Thu, 13 Aug 2015 18:09:04 +0900 (GMT) subject: Re: [Wien] Control of very small fraction of atoms in alloy 13.08.2015 06:46, Seongjae Cho пишет: So, a simple idea that struck me was it would be really good if there might be a way to put extrinsic atoms one by one into that already made supper cell having 100 or so basis atoms. Yes, this is a right way. With large supercells you should check, with a higher attention, a convergence of the calculation over calculational parameters (Rkmax, N k-points), over the values you want to study. Making calc parameters higher increases calculational time, so you should find a compromise between accuracy and the time. Best way is, first, to make a calcuation with lower parameters, then to increase them, and so forth. The accuracy, that you need to chose, depends strongly on your task. There is a huge set of papers made under WIEN2k http://www.wien2k.at/papers/index.html You can find there studies that may be compared with your task. Best wishes Lyudmila Dobysheva -- Phys.-Techn. Institute of Ural Br. of Russian Ac. of Sci. 426001 Izhevsk, ul.Kirova 132 RUSSIA -- Tel.:7(3412) 432045(office), 722529(Fax) E-mail: l...@ftiudm.ru, lyuk...@mail.ru (office) lyuk...@gmail.com (home) Skype: lyuka17 (home), lyuka18 (office) http://ftiudm.ru/content/view/25/103/lang,english/ -- ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
