Re: [Wien] (no subject)
Hello wasim, I4m not quite sure what happens by default but you should make sure that the wien directory is added to your global path (and that it is correct). Does /home/naushad/software/ contain the wien files or is it maybe a subdirectory /home/naushad/software/wien for instance then you could for instance do export WIENROOT= /home/naushad/software/wien and export PATH=$PATH:$WIENROOT (if you're working in bash) and it should find it. Maybe do echo $WIENROOT and echo $PATH to see what your current values are. A full overview of environment values can be found in section 11.4 of the manual. Regards, Michael Sluydts Op 9/04/2013 12:32, wasim raja Mondal schreef: Dear wien2k community, I am beginner in wien2k. I am running Tic example from the wien2k manual. After doing the structure generation successfully when I am doing initialization I am facing this problem: please help me. /home/naushad/software/nn: Command not found. 0.0u 0.0s 0:00.00 0.0% 0+0k 0+0io 0pf+0w error: command /home/naushad/software/nn nn.def failed ___ 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
[Wien] thanks
Dear users, I want to thank all users who have responded to my question and have proposed a solution to my problem. Dr Houda Ben Abdallah___ 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] A question on the lapw2
Hi, all: I met a problem in the calculation of Ni doped diamond supercell. Explicitly, what I'm trying to calculate is a 2x2x2 diamond supercell doped with a Nickel atom in the center of the supercell. Part of the structure files is pasted as follows: Ni_Diamond P 10 RELA 13.492650 13.492650 13.492650 90.00 90.00 90.00 ATOM 1: X=0. Y=0. Z=0. MULT= 1 ISPLIT= 2 C 1NPT= 781 R0=0.0001 RMT=1.3600 Z: 6.0 LOCAL ROT MATRIX:1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM -2: X=0.5000 Y=0. Z=0. MULT= 3 ISPLIT=-2 -2: X=0. Y=0.5000 Z=0. -2: X=0. Y=0. Z=0.5000 C 2NPT= 781 R0=0.0001 RMT=1.3600 Z: 6.0 LOCAL ROT MATRIX:0.000 0.000 1.000 1.000 0.000 0.000 0.000 1.000 0.000 ATOM -3: X=0.5000 Y=0.5000 Z=0. MULT= 3 ISPLIT=-2 -3: X=0.5000 Y=0. Z=0.5000 -3: X=0. Y=0.5000 Z=0.5000 C 3NPT= 781 R0=0.0001 RMT=1.3600 Z: 6.0 LOCAL ROT MATRIX:1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM 4: X=0.5000 Y=0.5000 Z=0.5000 MULT= 1 ISPLIT= 2 Ni4NPT= 781 R0=0.5000 RMT=1.7500 Z: 28.0 LOCAL ROT MATRIX:1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM -5: X=0.2500 Y=0.2500 Z=0. MULT=12 ISPLIT= 8 -5: X=0.7500 Y=0.2500 Z=0. -5: X=0.2500 Y=0.7500 Z=0. -5: X=0.7500 Y=0.7500 Z=0. -5: X=0.2500 Y=0. Z=0.2500 I used the parallel calculation mode and the whole program just crashed in the lapw2 step. In the output file, I have the following messages: LAPW1 END LAPW1 END LAPW2 - FERMI; weighs written forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PCRoutineLineSource forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PCRoutineLineSource lapw2c 0001000652A1 _l2main_ 893 l2main_tmp_.F lapw2c 0001000652A1 _l2main_ 893 l2main_tmp_.F lapw2c 0001000798E3 _MAIN__ 564 lapw2_tmp_.F lapw2c 0001141C Unknown Unknown Unknown lapw2c 0001000798E3 _MAIN__ 564 lapw2_tmp_.F lapw2c 000113D4 Unknown Unknown Unknown lapw2c 0001141C Unknown Unknown Unknown lapw2c 000113D4 Unknown Unknown Unknown forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PCRoutineLineSource lapw2c 0001000652A1 _l2main_ 893 l2main_tmp_.F lapw2c 0001000798E3 _MAIN__ 564 lapw2_tmp_.F lapw2c 0001141C Unknown Unknown Unknown lapw2c 000113D4 Unknown Unknown Unknown forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PCRoutineLineSource lapw2c 0001000652A1 _l2main_ 893 l2main_tmp_.F forrtl: severe (174): SIGSEGV, segmentation fault occurred lapw2c 0001000798E3 _MAIN__ 564 lapw2_tmp_.F Image PCRoutineLineSource lapw2c 0001141C Unknown Unknown Unknown lapw2c 0001000652A1 _l2main_ 893 l2main_tmp_.F lapw2c 000113D4 Unknown Unknown Unknown lapw2c 0001000798E3 _MAIN__ 564 lapw2_tmp_.F lapw2c 0001141C Unknown Unknown Unknown lapw2c 000113D4 Unknown Unknown Unknown forrtl: severe (174): SIGSEGV, segmentation fault occurred I checked the mailist and tried many possible solutions like decreasing the value of RMT*KMax. But they just doesn't work. I can paste the other configuration files if necessary. I really appreciate any suggestions or comments. Thank you in advance. Best, Wenhao ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at
Re: [Wien] Calculations at moderate T
a) Simply empirically extrapolate a0 to a possible value at 1200 K. b) Ab initio: quasiharmonic approximation. Calculate phonons (wien2k + ponon or phonopy, see u supported sw) and resulting -TS at various lattice parameters and search for the minimum of the free energy as function of a0 at the desired T Of course, for a surface this is more difficult. Of course one can use the expanded a,b lattice constants, but relaxation of z will still corrsepond to t=0. It is more a simulation of an epitactically expanded lattice. Am 09.04.2013 19:38, schrieb Laurence Marks: Does anyone know of methods to do calculations at T~1200K taking account of bulk thermal expansion? I am interested in a surface calculation where I suspect that it may be important to consider this, and a moderately rational approach to doing this that has been tested/published would be useful. -- - Peter Blaha Inst. Materials Chemistry, TU Vienna Getreidemarkt 9, A-1060 Vienna, Austria Tel: +43-1-5880115671 Fax: +43-1-5880115698 email: pbl...@theochem.tuwien.ac.at - ___ 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] Segmentation fault in lapw2 during slab calculation
Dear wien2k community, I have been doing a series of calculations for platinum slabs. 3, 5, 7, and 9 layers go through without a hitch, but I get a Segmentation fault in lapw2 in the first iteration of an scf when attempting 11 layers. The slabs were created with structeditor, and all of them had 30 bohr vacuum. OS: Mac OS X 10.7.5, case sensitive file system, 18GB RAM. I am running version 12.1 of wien2k. Compiler: Intel ifort 13.3.171 with associated MKL The segfault happens both for k-point parallel and serial runs. I get the same result if I run through the web interface or command line, so an example of a typical run looks like: $ init_lapw -b -red 5 -rkmax 6 -numk 1000 ... $ x lapw0 LAPW0 END $ x lapw1 LAPW1 END $ x lapw2 Segmentation fault (time info) error: command /Users/Anders/WIEN2k_12/lapw2 lapw2.def failed My OPTIONS file: current:FOPT:-O -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -g -traceback -check all current:FPOPT:-FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -DFFTW3 -traceback current:LDFLAGS:$(FOPT) -L$(MKLROOT)/lib -pthread current:DPARALLEL:'-DParallel' current:R_LIBS:-lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -openmp -lpthread -lm current:RP_LIBS:-L/opt/scalapack/lib/ -lscalapack -L/opt/fftw3/lib/ -lfftw3_mpi -lfftw3 $(R_LIBS) current:MPIRUN:mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_ NMATMAX = 3 NUME = 3000 By inserting write statements, I have figured out that the code makes it to just before the call to l2main in lapw2 (around line 570 in lapw2.F) -- a write statement directly after the declarations in l2main.F does not get printed. Even though I have -g -traceback in the compilation, I am uncertain how to extract the actual traceback information... Any help with figuring out what needs to be done to run this calculation would be much appreciated. Thank you, Anders Glans Pt06.struct.tgz Description: Binary data ___ 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] Calculations at moderate T
Thanks. Method a) is the only reasonable one, coupled with extrapolating the bulk reference lattice parameters. This would have to be done by a uniform volume expansion without relaxation of course. On Tue, Apr 9, 2013 at 3:03 PM, Peter Blaha pbl...@theochem.tuwien.ac.at wrote: a) Simply empirically extrapolate a0 to a possible value at 1200 K. b) Ab initio: quasiharmonic approximation. Calculate phonons (wien2k + ponon or phonopy, see u supported sw) and resulting -TS at various lattice parameters and search for the minimum of the free energy as function of a0 at the desired T Of course, for a surface this is more difficult. Of course one can use the expanded a,b lattice constants, but relaxation of z will still corrsepond to t=0. It is more a simulation of an epitactically expanded lattice. Am 09.04.2013 19:38, schrieb Laurence Marks: Does anyone know of methods to do calculations at T~1200K taking account of bulk thermal expansion? I am interested in a surface calculation where I suspect that it may be important to consider this, and a moderately rational approach to doing this that has been tested/published would be useful. -- - Peter Blaha Inst. Materials Chemistry, TU Vienna Getreidemarkt 9, A-1060 Vienna, Austria Tel: +43-1-5880115671 Fax: +43-1-5880115698 email: pbl...@theochem.tuwien.ac.at - ___ 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 -- 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@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] Segmentation fault in lapw2 during slab calculation
Also, and in general, if you are trying to track a problem comment out calls the W2kinit -- this routine can catch faults which is good for terminating mpi tasks, but can get in the way of debugging. On Tue, Apr 9, 2013 at 7:12 PM, Gavin Abo gs...@crimson.ua.edu wrote: In order to get traceback information in Mac OS X, I think you need to use different debug settings as described at: http://software.intel.com/en-us/articles/using-the-idb-debugger-under-mac-os-x-107-lion/ On 4/9/2013 5:34 PM, Anders Glans wrote: Dear wien2k community, I have been doing a series of calculations for platinum slabs. 3, 5, 7, and 9 layers go through without a hitch, but I get a Segmentation fault in lapw2 in the first iteration of an scf when attempting 11 layers. The slabs were created with structeditor, and all of them had 30 bohr vacuum. OS: Mac OS X 10.7.5, case sensitive file system, 18GB RAM. I am running version 12.1 of wien2k. Compiler: Intel ifort 13.3.171 with associated MKL The segfault happens both for k-point parallel and serial runs. I get the same result if I run through the web interface or command line, so an example of a typical run looks like: $ init_lapw -b -red 5 -rkmax 6 -numk 1000 ... $ x lapw0 LAPW0 END $ x lapw1 LAPW1 END $ x lapw2 Segmentation fault (time info) error: command /Users/Anders/WIEN2k_12/lapw2 lapw2.def failed My OPTIONS file: current:FOPT:-O -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -g -traceback -check all current:FPOPT:-FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -DFFTW3 -traceback current:LDFLAGS:$(FOPT) -L$(MKLROOT)/lib -pthread current:DPARALLEL:'-DParallel' current:R_LIBS:-lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -openmp -lpthread -lm current:RP_LIBS:-L/opt/scalapack/lib/ -lscalapack -L/opt/fftw3/lib/ -lfftw3_mpi -lfftw3 $(R_LIBS) current:MPIRUN:mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_ NMATMAX = 3 NUME = 3000 By inserting write statements, I have figured out that the code makes it to just before the call to l2main in lapw2 (around line 570 in lapw2.F) -- a write statement directly after the declarations in l2main.F does not get printed. Even though I have -g -traceback in the compilation, I am uncertain how to extract the actual traceback information... Any help with figuring out what needs to be done to run this calculation would be much appreciated. Thank you, Anders Glans ___ 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 -- 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@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
