[Wien] Fermi - Error in Band structure calculation
Hi Prof Blaha and Wien2k users, I am trying to calculate the spin polarized band structure of a semiconducting supercell with a transition metal impurity. It works fine when the calculation is performed without spin-orbit interaction but for spin-orbit it gives me the following error: running LAPW2 in parallel mode calculating QTL's from parallel vectors Fermi - Error The dnlapw2.error file reads: 'LAPW2' can't open unit: 30 LAPW2' - filename: Mn110.energysodn_9 I have used the following steps to calculate the band structure as instructed in the user manual: (the calculation was done using 8 processors) 1. Minimized the energy with spin-orbit interaction using runsp_lapw -p -i 200 -ec 0.1 -cc 0.001 -it0 -so 2. Calculated eigen values using band_klist for fcc crystal (111 k-points) using lapw1 -c -p -band -so -up lapw1 -c -p -band -so -dn 3. Calculated partial charges for band character plotting using lapw2 -c -p -band -qtl -so -up lapw2 -c -p -band -qtl -so -dn I have used the same steps to calculate band structure without -so and that worked fine, so I am not sure why I am getting the error message when I am using so. I would like to mention that the density of states calculation with spin-orbit works fine. Looking at the error message it occurred to me that for some reason lapw2 is looking for a file case.energysodn_9, even though I have submitted job in 8 processors. I would appreciate if anyone can tell me how to fix this problem Thanks, Fhokrul
[Wien] Question about MPI parallelization
Dear All, We are trying to calculate a big system with more than 200 atoms with MPI parallelization and we started with RKmax=3.5~4. GGA potential is used and it is magnetic system without inversion. We had MPI errors and have been tried to resolve this issue already a couple of weeks and still have not resolved the problems. We have the following setup. - 1) i) Hardware Xeon 5400 Series with Gigabit connection and 1-3 GB of memory per core ii) Opterons dual core Processor 8214 connected via Infiniband 2) Latest WIEN2K downloaded from the Wien2k website. Software: OS == SuSE 10.2 Compilers: Intel 9.1 Intel 10.1 Libraries: MKL 9.0 10.2 BLACS SCALAPACK for MKL 9.0 compiled separately and taken from intel MKL package for MKL 10.1 FFTW 2 3 Mpich 1.2.6 we have but not tested yet mpich2, opterons have mvapich 0.9.9 --- And test results are: first we compiled MKL 9.0 + Intel fortran 9.0 + BLACS+SCALAPACK +FFTW23 +MPICH1on XEON machines, And MKL 9.0 + Intel fortran 9.0 + BLACS+SCALAPACK +FFTW23 + MVAPICH on OPTERON machines Both gave us similar results: LAPW0 was OK every time. LAPW1 gives us the following problems: - 8 - NO ERROR MESSAGE : Could not convert index 101833776 into a pointer The index may be an incorrect argument. Possible sources of this problem are a missing include 'mpif.h', a misspelled MPI object (e.g., MPI_COM_WORLD instead of MPI_COMM_WORLD) or a misspelled user variable for an MPI object (e.g., com instead of comm). [8] [] Aborting Program! - OUTPUT from dayfile is : - Calculating mag in /mnt/parallel/30109udo/mag on n109 with PID 27390 start (Wed Sep 23 23:34:30 EDT 2009) with lapw0 (40/99 to go) lapw1 -c -up -p(23:39:26) starting parallel lapw1 at Wed Sep 23 23:39:26 EDT 2009 - starting parallel LAPW1 jobs at Wed Sep 23 23:39:26 EDT 2009 running LAPW1 in parallel mode (using .machines) 1 number_of_parallel_jobs n107 n107 n107 n107 n107 n107 n107 n107 n109 n109 n109 n109 n109 n109 n109 n109 n110 n110 n110 n110 n110 n110 n110 n110(5) command: n107 cd /parallel/30109udo/mag;time /opt/mvapich/intel_ud/bin/mpirun -np 24 -machin efile .machine1 /home/wien2k_09_ib//lapw1c_mpi uplapw1_1.def;rm -f.lock_n1071 rh: n107 cmd: cd /parallel/30109udo/mag;time /opt/mvapich/intel_ud/bin/mpirun -np 24 -machinefile .machine1 /home/wien2 k_09_ib//lapw1c_mpi uplapw1_1.def;rm -f .lock_n1071 /opt/SGE/bin/lx24-amd64/qrsh -V -inherit n107 cd /parallel/30109udo/mag;time /opt/mvapich/intel_ud/bin/mpirun -np 24 -machinefile .machine1 /home/wien2k_09_ib//lapw1c_mpi uplapw1_1.def;rm -f .lock_n1071 ** LAPW1 crashed! 0.084u 0.152s 0:07.48 3.0% 0+0k 0+0io 12pf+0w error: command /home/wien2k_09_ib/lapw1cpara -up -c uplapw1.def failed stop error If we change in BLACS configuration line: TRANSCOMM = -DUseMpich -DPOINTER_64_BITS=1 to TRANSCOMM = -DUseMpich it compiles and kind of works but it can crash usually after the first iteration given in vector files and in output2 files NaN which then causes LAPW2 to fail. For example for Inifiniband version output looks like this: LAPW0 END forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PCRoutineLineSource lapw1c_mpi 0097ADB8 Unknown Unknown Unknown lapw1c_mpi 009793FD Unknown Unknown Unknown lapw1c_mpi 004A8EE3 Unknown Unknown Unknown lapw1c_mpi 004E811C Unknown Unknown Unknown lapw1c_mpi 004C31B2 Unknown Unknown Unknown lapw1c_mpi 00475538 Unknown Unknown Unknown lapw1c_mpi 0048F18D Unknown Unknown Unknown lapw1c_mpi 004549CC seclr4_ 280 seclr4_tmp_.F lapw1c_mpi 00416BD0 calkpt_ 200 calkpt_tmp_.F lapw1c_mpi 0043C77D MAIN__ 60 lapw1_tmp_.F lapw1c_mpi 0040F0CA Unknown Unknown Unknown libc.so.6 2AFA1178FAE4 Unknown Unknown Unknown lapw1c_mpi 0040F015 Unknown Unknown Unknown 2) similar story we got with intel 10.1 compiles + MKL 10.2 + MKL 10.2 blacs and scalalapack + mpich1.
[Wien] Fermi - Error in Band structure calculation
You missed a step, see below: Fhokrul Islam schrieb: Hi Prof Blaha and Wien2k users, I am trying to calculate the spin polarized band structure of a semiconducting supercell with a transition metal impurity. It works fine when the calculation is performed without spin-orbit interaction but for spin-orbit it gives me the following error: running LAPW2 in parallel mode calculating QTL's from parallel vectors Fermi - Error The dnlapw2.error file reads: 'LAPW2' can't open unit: 30 LAPW2' - filename: Mn110.energysodn_9 I have used the following steps to calculate the band structure as instructed in the user manual: (the calculation was done using 8 processors) 1. Minimized the energy with spin-orbit interaction using runsp_lapw -p -i 200 -ec 0.1 -cc 0.001 -it0 -so 2. Calculated eigen values using band_klist for fcc crystal (111 k-points) using lapw1 -c -p -band -so -up lapw1 -c -p -band -so -dn lapw1 does NOT take a switch -so (see x lapw1 -h for possible options) after step 2 you need: x lapwso -up -p -c 3. Calculated partial charges for band character plotting using lapw2 -c -p -band -qtl -so -up lapw2 -c -p -band -qtl -so -dn I have used the same steps to calculate band structure without -so and that worked fine, so I am not sure why I am getting the error message when I am using so. I would like to mention that the density of states calculation with spin-orbit works fine. Looking at the error message it occurred to me that for some reason lapw2 is looking for a file case.energysodn_9, even though I have submitted job in 8 processors. I would appreciate if anyone can tell me how to fix this problem Thanks, Fhokrul ___ 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: +43-1-58801-15671 FAX: +43-1-58801-15698 Email: blaha at theochem.tuwien.ac.atWWW: http://info.tuwien.ac.at/theochem/ --
[Wien] Fermi - Error in Band structure calculation
Thank you very much for pointing out the mistake. From: wien-bounces at zeus.theochem.tuwien.ac.at [wien-bounces at zeus.theochem.tuwien.ac.at] On Behalf Of Peter Blaha [pbl...@theochem.tuwien.ac.at] Sent: 25 September 2009 09:19 To: A Mailing list for WIEN2k users Subject: Re: [Wien] Fermi - Error in Band structure calculation You missed a step, see below: Fhokrul Islam schrieb: Hi Prof Blaha and Wien2k users, I am trying to calculate the spin polarized band structure of a semiconducting supercell with a transition metal impurity. It works fine when the calculation is performed without spin-orbit interaction but for spin-orbit it gives me the following error: running LAPW2 in parallel mode calculating QTL's from parallel vectors Fermi - Error The dnlapw2.error file reads: 'LAPW2' can't open unit: 30 LAPW2' - filename: Mn110.energysodn_9 I have used the following steps to calculate the band structure as instructed in the user manual: (the calculation was done using 8 processors) 1. Minimized the energy with spin-orbit interaction using runsp_lapw -p -i 200 -ec 0.1 -cc 0.001 -it0 -so 2. Calculated eigen values using band_klist for fcc crystal (111 k-points) using lapw1 -c -p -band -so -up lapw1 -c -p -band -so -dn lapw1 does NOT take a switch -so (see x lapw1 -h for possible options) after step 2 you need: x lapwso -up -p -c 3. Calculated partial charges for band character plotting using lapw2 -c -p -band -qtl -so -up lapw2 -c -p -band -qtl -so -dn I have used the same steps to calculate band structure without -so and that worked fine, so I am not sure why I am getting the error message when I am using so. I would like to mention that the density of states calculation with spin-orbit works fine. Looking at the error message it occurred to me that for some reason lapw2 is looking for a file case.energysodn_9, even though I have submitted job in 8 processors. I would appreciate if anyone can tell me how to fix this problem Thanks, Fhokrul ___ 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: +43-1-58801-15671 FAX: +43-1-58801-15698 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] Planes in valence charge density
Dear Wien2k users, I am new user of Wien2k. I wish to plot valence charge density and difference in valence charge density (for 100, 110 and 001 planes) for WS2sample. The structure file is as follows: WS2 H LATTICE,NONEQUIV.ATOMS: 2194_P63/mmc MODE OF CALC=RELA unit=ang 5.958309 5.958309 23.287104 90.00 90.00120.00 ATOM -1: X=0. Y=0. Z=0.2500 MULT= 2 ISPLIT= 4 -1: X=0.6667 Y=0.3334 Z=0.7500 W NPT= 781 R0=0.0500 RMT=2.4100 Z: 74.0 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. Y=0. Z=0.6210 MULT= 4 ISPLIT= 4 -2: X=0.6667 Y=0.3334 Z=0.3790 -2: X=0.6667 Y=0. Z=0.1210 -2: X=0. Y=0.6667 Z=0.8790 S NPT= 781 R0=0.0001 RMT=2.1300 Z: 16.0 LOCAL ROT MATRIX:1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 24 NUMBER OF SYMMETRY OPERATIONS I am unable to locate the input for the specific plane in case.in5 file. I have also tried Xcrysden to plot it but again the identification of specific plane remains uncertain. Can you please guide me how to plot valence charge densities and difference density (crystalline minus superposed atomic densities) for specific planes? Thank you in advance. -- Alpa Dashora -- next part -- An HTML attachment was scrubbed... URL: http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20090925/fd3cf82e/attachment.htm
[Wien] Planes in valence charge densityalpa dashora escribió:
The best plane is (in file WS2.in5): 1 0 0 0 1 0 1 0 1/2 which is a vertical plane WS2.in5: 1 0 0 1 # x, y, z, divisorof origin 0 1 0 1 # x, y, z, divisorof x-end 2 0 1 2 # x, y, z, divisorof y-end 3 2 3 # number of shells 60 60# number of points in x and y dir, (ratio close to lenght ratio RHO # RHO|DIFF|OVER; ADD|SUB or blank ANG VAL NODEBUG # ANG|ATU; VAL|TOT; DEBUG|NODEBUG ORTHO # optional: ORHO|NONORTHO plotting directions Note that I put 60 60 so that using in the XTerm the 'rhoplot' you can move relatively fast. an horizontal plane would be 0 0 1/4 1 0 1/4 1 2 1/4 (one has to put orthogonal coordinates and this is an hexagonal system) 0 0 1 4 # x, y, z, divisorof origin 4 0 1 4 # x, y, z, divisorof x-end 4 8 1 4 # x, y, z, divisorof y-end I am new user of Wien2k. I wish to plot valence charge density and difference in valence charge density (for 100, 110 and 001 planes) for WS2 sample. The structure file is as follows: WS2 H LATTICE,NONEQUIV.ATOMS: 2194_P63/mmc MODE OF CALC=RELA unit=ang 5.958309 5.958309 23.287104 90.00 90.00120.00 ATOM -1: X=0. Y=0. Z=0.2500 MULT= 2 ISPLIT= 4 -1: X=0.6667 Y=0.3334 Z=0.7500 W NPT= 781 R0=0.0500 RMT=2.4100 Z: 74.0 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. Y=0. Z=0.6210 MULT= 4 ISPLIT= 4 -2: X=0.6667 Y=0.3334 Z=0.3790 -2: X=0.6667 Y=0. Z=0.1210 -2: X=0. Y=0.6667 Z=0.8790 S NPT= 781 R0=0.0001 RMT=2.1300 Z: 16.0 LOCAL ROT MATRIX:1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 24 NUMBER OF SYMMETRY OPERATIONS I am unable to locate the input for the specific plane in case.in5 file. I have also tried Xcrysden to plot it but again the identification of specific plane remains uncertain. Can you please guide me how to plot valence charge densities and difference density (crystalline minus superposed atomic densities) for specific planes? Thank you in advance. -- Alpa Dashora ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
[Wien] Surface states
Dear Francisco, How about checking partial DOS or fat bands for the surface atoms. You can draw your bulk calculation results on top of slab calculation results. If the thickness of bulk is enough, you can identify some bands which are similar to bulk one. And the variations from bulk can be thought as surface effects which proceed and dissipate from surface up to some layers into the center of slab. Usually for the very surface-wise atom, it looks quite different from bulk one because of the absence of neighbor. Kyoo. Department of Physics. Rutgers. -- next part -- An HTML attachment was scrubbed... URL: http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20090925/fe731687/attachment.htm
