[Wien] Crystal structure
Dear Antonio, Look at page 40 in the most recent version of Wien2k usersguide at http://www.wien2k.at/reg_user/textbooks/usersguide.pdf. In fact, you should specify the five direct coordinates of the five atoms in your basis in rhomohedral coordinates, but when specifying the unit cell, you enter the a_hex and c_hex lattice of the hexagonal envelope (see second figure at http://www.mx.iucr.org/iucr-top/comm/cteach/pamphlets/5/node3.html ) You can type your rhomohedral coordinates in a form at http://qpeng.org/tools/r2h.html but you should definitely check the results for yourself. Regards Tomas P?vodn? zpr?va Od: Antonio Vanderlei dos Santos - Fisica vandao at urisan.tche.br P?edm?t: [Wien] Crystal structure Datum: 14.5.2012 21:14:39 Dear users I'm trying to calculate the following structure. rhombohedra Crystal structure with the spacegroup (R3m) with Five atoms in one unit cell. Could someone provide me the correct atomic positions. regards
[Wien] non-corrolated orbitals and GGA+U approximation
Dear pro.Balha, we want to know if it is reasonable to use GGA+U for the non-corrolated orbitals like p orbitals? we have used GGA+U for O-2p and Zn-3d orbitals with Ud=0.98 Ry and Up=1.1Ry and in this case we obtained the band gap of ZnO ( wurtzite structure) 3.03 eV , which is very close to the experimental results.Also, we have used MBJLDA approximation and obtained the energy gap 2.2 eV, which is quite smaller than the value obtained using GGA+U approximation, although we expected to get an exact result with MBJLDA! thank you very much in advance `
[Wien] Problem to run Wien2k in parallel mode
Your .machines file is wrong. You are requesting a mpi calculation, but WIENncm is not mpi parallel. You can use only k-parallel calculations. Am 15.05.2012 21:00, schrieb Matheus Lessa .: Hello fellows, I've been trying to run Wien2k in parallel mode and, after finally succeed, inadvertently I delete the .Machines file and since then, I think because of that, I haven't more achieved run the application in parallel mode. In serial mode it usually occurs without errors. Does anyone have any idea what might be happening? Below is some information that may be important. OPTIONS File: current:FOPT:-FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback -I/opt/ intel/Compiler/11.1/080/mkl/lib/em64t -i-static current:FPOPT:-FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback -I/opt /intel/Compiler/11.1/080/mkl/include -i-static current:LDFLAGS:$(FOPT) -L/opt/intel/Compiler/11.1/080/mkl/lib/em64t -pthread -i -static current:DPARALLEL:'-DParallel' current:R_LIBS:-lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_cor e -openmp -lpthread -i-static current:RP_LIBS:-lmkl_scalapack_lp64 -lmkl_solver_lp64 -lmkl_blacs_lp64 -L/home/ admin/libs/fftw/lib/ -lfftw_mpi -lfftw $(R_LIBS) current:MPIRUN:mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_ .machines file: granularity:1 1:zumbi:4 1:no0:4 residue:zumbi The system is formed by two identical machines with: Intel Quad-Core processor, 8GB RAM Memory, Oracle Grid Engine,MPICH2 1.4 with MPD, Ifort 11.1 with MKL and FFTW, BLAS,BLACS,Lapack and Scalapack libraries. The Zumbi node is the main node. The error exit is: [admin at zumbi gaas]$ run_lapw -p LAPW0 END gaas.scf1_1: FNosuch file or directory FERMI - Error cp: impossible to get state of .in.tmp: Nosuch file or directory rm: wasn't possible to remove .in.tmp:Nosuch file or directory rm: wasn't possible to remove .in.tmp1: Nosuch file or directory stop error lapw2.error file Error in LAPW2 'LAPW2' - can't open unit: 30 'LAPW2' - filename: gaas.energy_1 ** testerror: Error in Parallel LAPW2 P.S: The compilation occurs without errors or warnings Thanks foreveryone's attention. MLessa Computer Science Student FederalUniversityofBahia ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- P.Blaha -- Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna Phone: +43-1-58801-165300 FAX: +43-1-58801-165982 Email: blaha at theochem.tuwien.ac.atWWW: http://info.tuwien.ac.at/theochem/ --
[Wien] non-corrolated orbitals and GGA+U approximation
With LDA+U you can do almost anything by choosing some parameters (try negative U,) and thus, if you know the experiment, you can play around and vary U of some atoms and states until you get the desired result (you could probably also use a larger U on Zn and a smaller one on O and get the same gap). The question is always: is it physical reasonable and justified, or is it just a dirty fix to reproduce some experimental value. The answer to this question is not that simple. For sure, in GGA also the O-p states are not treated 100% correctly, but they should be better than the Zn-d states. Thus, personally I don't like a calculation with U(O-p)=1.1 Ry. In addition, remember that even the exact DFT functional (if we ever get to know it), would NOT give you the correct gap. Am 16.05.2012 11:23, schrieb masoud majidiyan: Dear pro.Balha, we want to know if it is reasonable to use GGA+U for the non-corrolated orbitals like p orbitals? we have used GGA+U for O-2p and Zn-3d orbitals with Ud=0.98 Ry and Up=1.1Ry and in this case we obtained the band gap of ZnO ( wurtzite structure) 3.03 eV , which is very close to the experimental results.Also, we have used MBJLDA approximation and obtained the energy gap 2.2 eV, which is quite smaller than the value obtained using GGA+U approximation, although we expected to get an exact result with MBJLDA! thank you very much in advance ` ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- P.Blaha -- Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna Phone: +43-1-58801-165300 FAX: +43-1-58801-165982 Email: blaha at theochem.tuwien.ac.atWWW: http://info.tuwien.ac.at/theochem/ --
[Wien] non-corrolated orbitals and GGA+U approximation
Just to be more specific: yes, the exact DFT potential would not give the correct gap. However, this statement applies for the case of orbital-independent potentials (like MBJLDA), while LDA+U is an orbital-dependent potential. On Wed, 16 May 2012, Peter Blaha wrote: With LDA+U you can do almost anything by choosing some parameters (try negative U,) and thus, if you know the experiment, you can play around and vary U of some atoms and states until you get the desired result (you could probably also use a larger U on Zn and a smaller one on O and get the same gap). The question is always: is it physical reasonable and justified, or is it just a dirty fix to reproduce some experimental value. The answer to this question is not that simple. For sure, in GGA also the O-p states are not treated 100% correctly, but they should be better than the Zn-d states. Thus, personally I don't like a calculation with U(O-p)=1.1 Ry. In addition, remember that even the exact DFT functional (if we ever get to know it), would NOT give you the correct gap. Am 16.05.2012 11:23, schrieb masoud majidiyan: Dear pro.Balha, we want to know if it is reasonable to use GGA+U for the non-corrolated orbitals like p orbitals? we have used GGA+U for O-2p and Zn-3d orbitals with Ud=0.98 Ry and Up=1.1Ry and in this case we obtained the band gap of ZnO ( wurtzite structure) 3.03 eV , which is very close to the experimental results.Also, we have used MBJLDA approximation and obtained the energy gap 2.2 eV, which is quite smaller than the value obtained using GGA+U approximation, although we expected to get an exact result with MBJLDA! thank you very much in advance ` ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- P.Blaha -- Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna Phone: +43-1-58801-165300 FAX: +43-1-58801-165982 Email: blaha at theochem.tuwien.ac.atWWW: http://info.tuwien.ac.at/theochem/ -- ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
[Wien] problem in wien2k 11 installation
Dear ? Prof P. Blaha ? I have installed WIEN2k 11 with composer_xe_2011_sp1.9.293 in my dell inspiron 1525 core2duo laptop. There were no errors encountered during the compilation. But when I tried to run TiC I got the following message ? /home/james/wien2k/lapw0: error while loading shared libraries: libmkl_intel_lp64.so: cannot open shared object file: No such file or directory stop error ?I have also asked in previous mail and instructed me set?the missing?path in?my .bashrc with the line: export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/intel/composer_xe_2011_sp1.9.293/mkl/lib/intel64 ? Unfortunately it does not work. Is WIEN2k 11 not compatable with core2duo machines? ? I have also problem in installation of wien2k 11 in my HP pavillion?core i3 desktop. Here the error message is ? /home/james/wien2k/lapw0: error while loading shared libraries: libmkl_lapack.so: ? stop error ? please help ? Jameson Maibam Assam University -- next part -- An HTML attachment was scrubbed... URL: http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20120516/cbc89d33/attachment.htm
[Wien] problem in wien2k 11 installation
Did you run userconfig_lapw ??? Do you include the source ...intel-config files and source mkl-files in your bashrc file ? (see some recent instructions how these files are actually called). Clearly, something is wrong with your environment. The error clearly says that when it wants to execute lapw0, it does not know where the mkl-library files are and you have to provide a proper environment, so that it knows this. Am 16.05.2012 12:28, schrieb Jameson Maibam: Dear Prof P. Blaha I have installed WIEN2k 11 with composer_xe_2011_sp1.9.293 in my dell inspiron 1525 core2duo laptop. There were no errors encountered during the compilation. But when I tried to run TiC I got the following message /home/james/wien2k/lapw0: error while loading shared libraries: libmkl_intel_lp64.so: cannot open shared object file: No such file or directory stop error I have also asked in previous mail and instructed me set the missing path in my .bashrc with the line: export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/intel/composer_xe_2011_sp1.9.293/mkl/lib/intel64 Unfortunately it does not work. Is WIEN2k 11 not compatable with core2duo machines? I have also problem in installation of wien2k 11 in my HP pavillion core i3 desktop. Here the error message is /home/james/wien2k/lapw0: error while loading shared libraries: libmkl_lapack.so: stop error please help Jameson Maibam Assam University ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- P.Blaha -- Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna Phone: +43-1-58801-165300 FAX: +43-1-58801-165982 Email: blaha at theochem.tuwien.ac.atWWW: http://info.tuwien.ac.at/theochem/ --
[Wien] arrows program on Windows
Dear WIEN2k experts, I'm trying to view forces on atoms using *arrows *utility in WIEN2k package (version 9.2). I followed the instructions in the corresponding version of WIEN2k user's guide. I copied my /case.struct /and /case.scf /to /case_initial.struct/ and /case_initial.scf/ respectively. Then I viewed the structure using XCrysDen program (version 1.4) in Windows through X-server and saved the structure as /case_initial.xsf/ file. The command 'x arrow' finished successfully, and it generated *case_initial.forces* file, but in the UG it says that the file should be case_forces.xsf. I tried both commands: xcrysden --xsf case forces.xsf or xcrysden --xsf case_initial.forces As a result I cannot see neither structure nor forces (empty screen in xcrysden). I believe that the problem is connected with the names of the file with forces, but I cannot identify correct name. Could anybody help me to make it working? Should I attach any files? Thanks, Maxim -- Best regards, Maxim Rakitin SUSU, Chelyabinsk, Russia email: rms85 at physics.susu.ac.ru web: http://www.susu.ac.ru -- next part -- An HTML attachment was scrubbed... URL: http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20120516/67d2e91f/attachment.htm
[Wien] Wienncm
On 11.05.2012 22:12, Hena Das wrote: (2) In lapw1.error: ** Error in Parallel LAPW1 ** LAPW1 STOPPED at Fri May 11 11:51:59 EDT 2012 On 14.05.2012 20:19, Hena Das wrote: I tried to do without -p option, i.e serial run, it works perfect. I think the problem is in parallel run On 15.05.2012 19:58, Hena Das wrote: 2. Look in output1 and all other files that should be written by lapw1 of ncm. The program completed law0 and made the corresponding output files. However, output1 files had not been created, it might indicates lapw1 crashed at the beginning. As far as I understood lapw1 does not create any file, lapw1.error also, is it correct? Try to find the diagnostic, for example in my computer, a program sends a copy of diagnostic to the file /var/mail/my_account. Look in your system the file /var/mail/your_account maybe there is a letter from computer. I suspect that somewhere is a diagnostic like error while loading shared libraries Best wishes Lyudmila Dobysheva -- Phys.-Techn. Institute of Ural Br. of Russian Ac. of Sci. 426001 Izhevsk, ul.Kirova 132 RUSSIA -- Tel.:7(3412) 442118 (home), 218988(office), 250614(Fax) E-mail: lyu at otf.pti.udm.ru lyuka17 at mail.ru Skype: lyuka17, lyuka18 http://fti.udm.ru/content/view/25/103/lang,english/ --
[Wien] ROTDEF error at lapw0 when applying mode distortion
Dear Prof. Blaha, thank you very much for your answer. The error in case.output0 appears only for the structure with a distortion of 0.15 (the second structure). The warnings in nn and sgroup take place because the structure has not actually symmetry Cmc21, but Fmm2. To do the initialization, I break the symmetry slightly, and no warnings appear. Then I remove the distortion and run the scf cycle, that is where I get the problem. Anyway I just took the 0.15 file and initalized directly; I got warnings in nn and sgroup; I refused to take the alternative file created by sgroup and sent the scf cycle after finishing the initialization. I got the same ROTDEF error in the case.outpu0 file. After reading your reply it seems that for some reason,the program does recognize the small distortion of the z position in atom 2 0.5859420 0.750 0.5003750 and it does for 0.4140580 0.250 0.0003750 can this have something to do with tolerance in sgroup? Maybe other reason? I am using WIEN2k 11 version and default accuracy parameters. Thank you very much in advance again. Regards Urko El 16/05/2012, a las 16:30, Peter Blaha escribi?: Well, you seem to trick WIEN's symmetry anyway, at least none of the programs nn and sgroup pass your struct files without error. Anyway, if one knows what one does, this can still be ok. The problem is, I cannot verify your error message 'ROTDEF' - no symmetry operation found. 'ROTDEF' - for jatom, index 2 4 'ROTDEF' - atomposition of jatom 0.5859420 0.750 0.500 'ROTDEF' - atomposition of index 0.4140580 0.250 0.0003750 with the 3 struct files you included. And it seems rather clear, that in the struct file which fails (not the one in your mail !!!) you have an error in your positions: Your undistorted struct file has: ATOM -2: X=0.58594200 Y=0.7500 Z=0.5000 MULT= 4 ISPLIT= 8 ATOM -2:X= 0.41405800 Y=0.2500 Z=0. ATOM -2:X= 0.41405800 Y=0.7500 Z=0.5000 ATOM -2:X= 0.58594200 Y=0.2500 Z=0. while the one which is supposed to show the error has: ATOM -2: X=0.58594200 Y=0.7500 Z=0.50037500 MULT= 4 ISPLIT= 8 ATOM -2:X= 0.41405800 Y=0.2500 Z=0.00037500 ATOM -2:X= 0.41405800 Y=0.7500 Z=0.50037500 ATOM -2:X= 0.58594200 Y=0.2500 Z=0.00037500 Your error (see above) gives z-position 0.5 and 0.000375, and of course for this mix you should get an error, as it seems that only one of the 2(or 4) positions has got modified in your struct file. Am 16.05.2012 12:31, schrieb urko petralanda holguin: Dear wien2k users, I am trying to do a frozen phonon calculation in SBN (SrBi2Nb2Ta9). When I try to calculate energies of the system with distortions proportional to the (polar) mode gm5, some problems appear. To perform the initialization I apply the high symmetry system (I4/mmm) a very small distortion, getting a Cmc21 (group 36) structure (I use this low symmetry configuraiton to be able to compare energies with other mode distortions at the end). After initializing, I remove this small distortion and then create the distorted struct files for different amplitudes of the mode, alongside the corresponding fphonons.job file. The calculation starts fine, reaching convergence in the energy calculation of the 0.00 (no distortion) case, but when jumping to the first distorted case it stops, giving the following error [urko at lcpxdf gm5th2]$ cat lapw0.error ** Error in Parallel lapw0 ** lapw0 STOPPED at lun may 14 22:09:46 CEST 2012 ** check ERROR FILES! The STDOUT file shows something like: [urko at lcpxdf gm5th2]$ tail -10 STDOUT ec cc and fc_conv 1 1 1 stop Fallback to compatibility mode with old save_lapw broyden files deleted, clm*, dmat*, vorb*, vresp*, eece*, scf and struct files saved under gm5th2_mode__0.00 ROTDEF - Error cat: No match. stop error ERROR status in gm5th2_mode__0.15 And the output files with errors are: [urko at lcpxdf gm5th2]$ cat gm5th2.output0 'ROTDEF' - no symmetry operation found. 'ROTDEF' - for jatom, index 2 4 'ROTDEF' - atomposition of jatom 0.5859420 0.750 0.500 'ROTDEF' - atomposition of index 0.4140580 0.250 0.0003750 After getting this error, I decided to try to run scf cycles for each distortion in different directories. I took a file with an amplitude of distortion of 0.15 angstroms and another one with an amplitude of 0.30. As expected, the first one gave the same ROTDEF ERROR in STDOUT, and in case.output0 but the second one (amplitude of 0.30) WENT FINE, reaching convergence. No errors appeared in the output or STDOUT files in this latter case.This makes me think that the problem arises for structures near high symmetry. The rest of the relevant parameters I use are: RKmax=6.5; 27 k points (div: 5 5 5). I attach the fphonons.job file, where the kind of run_lapw calculation is shown. I would be
