[Wien] Segmentation fault in Supercell Calculation
Dear WIEN2k user: I am using wien2k_14.2 on CentOS release 5.8. ifort version 12.1.3 with MKL. After generating a 2x2x1 supercell with 30 atoms, I tried to do the scf calculation. However, I got some errors. I'v attached it at the end of this email. My wien2k was installed correctly. It works well for other calculations. It also worked if I run non-parallel calculation for supercell. I'v searched the mail-list, but can't find any solutions. Could you give me a hint on how to solve the problem? Thank you very much. Sincerely Wangwei Lan On lapw0.error shows: 'Unknown' - SIGSEGV On super.dayfile shows: Child id 0 SIGSEGV Child id 8 SIGSEGV Child id 18 SIGSEGV Child id 23 SIGSEGV Child id 17 SIGSEGV On Screen shows: w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault -- MPI_ABORT was invoked on rank 18 in communicator MPI_COMM_WORLD with errorcode 451782144. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- -- mpirun has exited due to process rank 18 with PID 26388 on node corfu.magnet.fsu.edu exiting without calling "finalize". This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -- [corfu.magnet.fsu.edu:26369] 23 more processes have sent help message help-mpi-api.txt / mpi-abort [corfu.magnet.fsu.edu:26369] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages > stop error ___ 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 Supercell Calculation
Dear Professor Marks: I've check everything you have mentioned, they are all fine, nevertheless it still don't work. I think the input files are ok since I have no problem running in non-parallel mode. I tried to make the supercell smaller (2x1x1), then it works. However, I don't know why that happens. By the way, I have "ulimit -s unlimited " in my .bashrc file. I'v also adjusted the RKMAX and RMT before. Sincerely Wangwei Lan From: wien-boun...@zeus.theochem.tuwien.ac.at on behalf of Laurence Marks Sent: Tuesday, July 28, 2015 13:09 To: A Mailing list for WIEN2k users Subject: Re: [Wien] Segmentation fault in Supercell Calculation You have what is called a "Segmentation Violation" which was detected by 4 of the nodes and they called an error handler which stopped the mpi job on all the CPU's. This is normally because you have an error of some sort in your input files, any of case.in0, case.clmsum (and clmup/dn if you are using spin polarized). 1) Check that you do not have overlapping spheres and/or other mistakes. 2) Check your error files, e.g. "cat *.error". Are any others (e.g. dstart.error) not empty? Did you ignore an error during setup? 3) Check the lapw0 output in case.output0* -- maybe shows what is wrong. There are many possible sources, you have to find the specific one. On Tue, Jul 28, 2015 at 12:57 PM, Lan, Wangwei mailto:wl...@my.fsu.edu>> wrote: Dear WIEN2k user: I am using wien2k_14.2 on CentOS release 5.8. ifort version 12.1.3 with MKL. After generating a 2x2x1 supercell with 30 atoms, I tried to do the scf calculation. However, I got some errors. I'v attached it at the end of this email. My wien2k was installed correctly. It works well for other calculations. It also worked if I run non-parallel calculation for supercell. I'v searched the mail-list, but can't find any solutions. Could you give me a hint on how to solve the problem? Thank you very much. Sincerely Wangwei Lan On lapw0.error shows: 'Unknown' - SIGSEGV On super.dayfile shows: Child id 0 SIGSEGV Child id 8 SIGSEGV Child id 18 SIGSEGV Child id 23 SIGSEGV Child id 17 SIGSEGV On Screen shows: w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault -- MPI_ABORT was invoked on rank 18 in communicator MPI_COMM_WORLD with errorcode 451782144. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- -- mpirun has exited due to process rank 18 with PID 26388 on node corfu.magnet.fsu.edu<http://corfu.magnet.fsu.edu> exiting without calling "finalize". This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -- [corfu.magnet.fsu.edu:26369<http://corfu.magnet.fsu.edu:26369>] 23 more processes have sent help message help-mpi-api.txt / mpi-abort [corfu.magnet.fsu.edu:26369<http://corfu.magnet.fsu.edu:26369>] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages > stop error -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu<http://www.numis.northwestern.edu> Corrosion in 4D: MURI4D.numis.northwestern.edu<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 ___ 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 Supercell Calculation
Dear Professor: Yes, "x lapw0" works without mpi. My mpi compile : mpif90 I use Open MPI， version 1.4.5 the parallel compilation options are -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback -assume buffered_io I use Intel MKL libraries, that part should be fine. Thanks very much for your help. Sincerely Wangwei Lan From: wien-boun...@zeus.theochem.tuwien.ac.at on behalf of Laurence Marks Sent: Tuesday, July 28, 2015 14:30 To: A Mailing list for WIEN2k users Subject: Re: [Wien] Segmentation fault in Supercell Calculation Does a simple "x lapw0" work, i.e. without mpi, for this specific case? If it does then there is probably an error in how you have linked/compiled the mpi versions. Please provide: a) The mpi compiler you used. b) Which type of mpi you are using (openmpi, mvapich, intel mpi etc) c) The parallel compilation options. N.B., a useful resource is https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor N.N.B., ulimit -s is not needed, this is (now) done in the software. On Tue, Jul 28, 2015 at 2:22 PM, Lan, Wangwei mailto:wl...@my.fsu.edu>> wrote: Dear Professor Marks: I've check everything you have mentioned, they are all fine, nevertheless it still don't work. I think the input files are ok since I have no problem running in non-parallel mode. I tried to make the supercell smaller (2x1x1), then it works. However, I don't know why that happens. By the way, I have "ulimit -s unlimited " in my .bashrc file. I'v also adjusted the RKMAX and RMT before. Sincerely Wangwei Lan From: wien-boun...@zeus.theochem.tuwien.ac.at<mailto:wien-boun...@zeus.theochem.tuwien.ac.at> mailto:wien-boun...@zeus.theochem.tuwien.ac.at>> on behalf of Laurence Marks mailto:l-ma...@northwestern.edu>> Sent: Tuesday, July 28, 2015 13:09 To: A Mailing list for WIEN2k users Subject: Re: [Wien] Segmentation fault in Supercell Calculation You have what is called a "Segmentation Violation" which was detected by 4 of the nodes and they called an error handler which stopped the mpi job on all the CPU's. This is normally because you have an error of some sort in your input files, any of case.in0, case.clmsum (and clmup/dn if you are using spin polarized). 1) Check that you do not have overlapping spheres and/or other mistakes. 2) Check your error files, e.g. "cat *.error". Are any others (e.g. dstart.error) not empty? Did you ignore an error during setup? 3) Check the lapw0 output in case.output0* -- maybe shows what is wrong. There are many possible sources, you have to find the specific one. On Tue, Jul 28, 2015 at 12:57 PM, Lan, Wangwei mailto:wl...@my.fsu.edu>> wrote: Dear WIEN2k user: I am using wien2k_14.2 on CentOS release 5.8. ifort version 12.1.3 with MKL. After generating a 2x2x1 supercell with 30 atoms, I tried to do the scf calculation. However, I got some errors. I'v attached it at the end of this email. My wien2k was installed correctly. It works well for other calculations. It also worked if I run non-parallel calculation for supercell. I'v searched the mail-list, but can't find any solutions. Could you give me a hint on how to solve the problem? Thank you very much. Sincerely Wangwei Lan On lapw0.error shows: 'Unknown' - SIGSEGV On super.dayfile shows: Child id 0 SIGSEGV Child id 8 SIGSEGV Child id 18 SIGSEGV Child id 23 SIGSEGV Child id 17 SIGSEGV On Screen shows: w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault -- MPI_ABORT was invoked on rank 18 in communicator MPI_COMM_WORLD with errorcode 451782144. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- -- mpirun has exited due to process rank 18 with PID 26388 on node corfu.magnet.fsu.edu<http://corfu.magnet.fsu.edu> exiting without calling "finalize". This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -- [corfu.magnet.fsu.edu:26369<http://corfu.magnet.fsu.edu:26369>] 23
Re: [Wien] Segmentation fault in Supercell Calculation
Dear sir: I don't quite understand how you did to solve the problem. Do you mean when you encounter this problem. Just run init_lapw again then scf calculation should work? Thanks very much. Sincerely Wangwei Lan From: wien-boun...@zeus.theochem.tuwien.ac.at on behalf of sikander Azam Sent: Tuesday, July 28, 2015 14:36 To: A Mailing list for WIEN2k users Subject: Re: [Wien] Segmentation fault in Supercell Calculation Dear sir, Mostly I also get the same problem, what I do, leave the struct . file and again do the initialization and then it's run well. Regards On 28 Jul 2015 21:25, "Lan, Wangwei" mailto:wl...@my.fsu.edu>> wrote: Dear Professor Marks: I've check everything you have mentioned, they are all fine, nevertheless it still don't work. I think the input files are ok since I have no problem running in non-parallel mode. I tried to make the supercell smaller (2x1x1), then it works. However, I don't know why that happens. By the way, I have "ulimit -s unlimited " in my .bashrc file. I'v also adjusted the RKMAX and RMT before. Sincerely Wangwei Lan From: wien-boun...@zeus.theochem.tuwien.ac.at<mailto:wien-boun...@zeus.theochem.tuwien.ac.at> mailto:wien-boun...@zeus.theochem.tuwien.ac.at>> on behalf of Laurence Marks mailto:l-ma...@northwestern.edu>> Sent: Tuesday, July 28, 2015 13:09 To: A Mailing list for WIEN2k users Subject: Re: [Wien] Segmentation fault in Supercell Calculation You have what is called a "Segmentation Violation" which was detected by 4 of the nodes and they called an error handler which stopped the mpi job on all the CPU's. This is normally because you have an error of some sort in your input files, any of case.in0, case.clmsum (and clmup/dn if you are using spin polarized). 1) Check that you do not have overlapping spheres and/or other mistakes. 2) Check your error files, e.g. "cat *.error". Are any others (e.g. dstart.error) not empty? Did you ignore an error during setup? 3) Check the lapw0 output in case.output0* -- maybe shows what is wrong. There are many possible sources, you have to find the specific one. On Tue, Jul 28, 2015 at 12:57 PM, Lan, Wangwei mailto:wl...@my.fsu.edu>> wrote: Dear WIEN2k user: I am using wien2k_14.2 on CentOS release 5.8. ifort version 12.1.3 with MKL. After generating a 2x2x1 supercell with 30 atoms, I tried to do the scf calculation. However, I got some errors. I'v attached it at the end of this email. My wien2k was installed correctly. It works well for other calculations. It also worked if I run non-parallel calculation for supercell. I'v searched the mail-list, but can't find any solutions. Could you give me a hint on how to solve the problem? Thank you very much. Sincerely Wangwei Lan On lapw0.error shows: 'Unknown' - SIGSEGV On super.dayfile shows: Child id 0 SIGSEGV Child id 8 SIGSEGV Child id 18 SIGSEGV Child id 23 SIGSEGV Child id 17 SIGSEGV On Screen shows: w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault -- MPI_ABORT was invoked on rank 18 in communicator MPI_COMM_WORLD with errorcode 451782144. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- -- mpirun has exited due to process rank 18 with PID 26388 on node corfu.magnet.fsu.edu<http://corfu.magnet.fsu.edu> exiting without calling "finalize". This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -- [corfu.magnet.fsu.edu:26369<http://corfu.magnet.fsu.edu:26369>] 23 more processes have sent help message help-mpi-api.txt / mpi-abort [corfu.magnet.fsu.edu:26369<http://corfu.magnet.fsu.edu:26369>] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages > stop error -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu<http://www.numis.northwestern.edu> Corrosion in 4D: MURI4D.numis.northwestern.ed
Re: [Wien] Segmentation fault in Supercell Calculation
Dear Professor: When I type "mpif90 --version", it give me " ifort (IFORT) 12.1.3 20120212". So, I thought it should work. My Libraries linking are listed below: Parallel excution: FFTW_LIB + FFTW_OPT: -lfftw3_mpi -lfftw3 -L/opt/fftw3.3.3/lib + -DFFTW3 -I/opt/fftw3.3.3/include (already set) RP RP_LIB(SCALAPACK+PBLAS): -lmkl_scalapack_lp64 -lmkl_blacs_lp64 $(R_LIBS) FP FPOPT(par.comp.options): -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback -assume buffered_io Compiler Option O Compiler options:-FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback -assume buffered_io -C -g F FFTW options:-DFFTW3 -I/opt/fftw3.3.3/include L Linker Flags:$(FOPT) -L$(MKLROOT)/lib/$(MKL_TARGET_ARCH) -pthread P Preprocessor flags '-DParallel' R R_LIB (LAPACK+BLAS): -lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lmkl_solver_lp64 FL FFTW_LIBS: -lfftw3_mpi -lfftw3 -L/opt/fftw3.3.3/lib Sincerely Wangwei From: wien-boun...@zeus.theochem.tuwien.ac.at on behalf of Laurence Marks Sent: Tuesday, July 28, 2015 14:59 To: A Mailing list for WIEN2k users Subject: Re: [Wien] Segmentation fault in Supercell Calculation Your options are probably wrong: a) mpif90 is normally gfortran, the Intel version is mpiifort b) It is easy to use the wrong linking with the Intel mkl libraries. Please provide the information I requested. On Tue, Jul 28, 2015 at 2:55 PM, Lan, Wangwei mailto:wl...@my.fsu.edu>> wrote: Dear Professor: Yes, "x lapw0" works without mpi. My mpi compile : mpif90 I use Open MPI， version 1.4.5 the parallel compilation options are -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback -assume buffered_io I use Intel MKL libraries, that part should be fine. Thanks very much for your help. Sincerely Wangwei Lan From: wien-boun...@zeus.theochem.tuwien.ac.at<mailto:wien-boun...@zeus.theochem.tuwien.ac.at> mailto:wien-boun...@zeus.theochem.tuwien.ac.at>> on behalf of Laurence Marks mailto:l-ma...@northwestern.edu>> Sent: Tuesday, July 28, 2015 14:30 To: A Mailing list for WIEN2k users Subject: Re: [Wien] Segmentation fault in Supercell Calculation Does a simple "x lapw0" work, i.e. without mpi, for this specific case? If it does then there is probably an error in how you have linked/compiled the mpi versions. Please provide: a) The mpi compiler you used. b) Which type of mpi you are using (openmpi, mvapich, intel mpi etc) c) The parallel compilation options. N.B., a useful resource is https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor N.N.B., ulimit -s is not needed, this is (now) done in the software. On Tue, Jul 28, 2015 at 2:22 PM, Lan, Wangwei mailto:wl...@my.fsu.edu>> wrote: Dear Professor Marks: I've check everything you have mentioned, they are all fine, nevertheless it still don't work. I think the input files are ok since I have no problem running in non-parallel mode. I tried to make the supercell smaller (2x1x1), then it works. However, I don't know why that happens. By the way, I have "ulimit -s unlimited " in my .bashrc file. I'v also adjusted the RKMAX and RMT before. Sincerely Wangwei Lan From: wien-boun...@zeus.theochem.tuwien.ac.at<mailto:wien-boun...@zeus.theochem.tuwien.ac.at> mailto:wien-boun...@zeus.theochem.tuwien.ac.at>> on behalf of Laurence Marks mailto:l-ma...@northwestern.edu>> Sent: Tuesday, July 28, 2015 13:09 To: A Mailing list for WIEN2k users Subject: Re: [Wien] Segmentation fault in Supercell Calculation You have what is called a "Segmentation Violation" which was detected by 4 of the nodes and they called an error handler which stopped the mpi job on all the CPU's. This is normally because you have an error of some sort in your input files, any of case.in0, case.clmsum (and clmup/dn if you are using spin polarized). 1) Check that you do not have overlapping spheres and/or other mistakes. 2) Check your error files, e.g. "cat *.error". Are any others (e.g. dstart.error) not empty? Did you ignore an error during setup? 3) Check the lapw0 output in case.output0* -- maybe shows what is wrong. There are many possible sources, you have to find the specific one. On Tue, Jul 28, 2015 at 12:57 PM, Lan, Wangwei mailto:wl...@my.fsu.edu>> wrote: Dear WIEN2k user: I am using wien2k_14.2 on CentOS release 5.8. ifort version 12.1.3 with MKL. After generating a 2x2x1 supercell with 30 atoms, I tried to do the scf calculation. However, I got some errors. I'v attached it at the end of this email. My wien2k was installed correctly. It works well for other calculations. It also worked if I run non-
Re: [Wien] Segmentation fault in Supercell Calculation
Dear professor: I use Open MPI, version 1.4.5. I added "-C -g" because some people in the mail-list said it probably will solve the problem. Thanks for your advice, I will recompile the package soon. Sincerely Wangwei From: wien-boun...@zeus.theochem.tuwien.ac.at on behalf of Laurence Marks Sent: Tuesday, July 28, 2015 15:36 To: A Mailing list for WIEN2k users Subject: Re: [Wien] Segmentation fault in Supercell Calculation N.B., unless you are a code developer "-C -g" are a terrible idea. Remove them, they may easily lead to the code crashing. Replace them by just "-O1" On Tue, Jul 28, 2015 at 3:28 PM, Lan, Wangwei mailto:wl...@my.fsu.edu>> wrote: Dear Professor: When I type "mpif90 --version", it give me " ifort (IFORT) 12.1.3 20120212". So, I thought it should work. My Libraries linking are listed below: Parallel excution: FFTW_LIB + FFTW_OPT: -lfftw3_mpi -lfftw3 -L/opt/fftw3.3.3/lib + -DFFTW3 -I/opt/fftw3.3.3/include (already set) RP RP_LIB(SCALAPACK+PBLAS): -lmkl_scalapack_lp64 -lmkl_blacs_lp64 $(R_LIBS) FP FPOPT(par.comp.options): -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback -assume buffered_io Compiler Option O Compiler options:-FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback -assume buffered_io -C -g F FFTW options:-DFFTW3 -I/opt/fftw3.3.3/include L Linker Flags:$(FOPT) -L$(MKLROOT)/lib/$(MKL_TARGET_ARCH) -pthread P Preprocessor flags '-DParallel' R R_LIB (LAPACK+BLAS): -lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lmkl_solver_lp64 FL FFTW_LIBS: -lfftw3_mpi -lfftw3 -L/opt/fftw3.3.3/lib Sincerely Wangwei From: wien-boun...@zeus.theochem.tuwien.ac.at<mailto:wien-boun...@zeus.theochem.tuwien.ac.at> mailto:wien-boun...@zeus.theochem.tuwien.ac.at>> on behalf of Laurence Marks mailto:l-ma...@northwestern.edu>> Sent: Tuesday, July 28, 2015 14:59 To: A Mailing list for WIEN2k users Subject: Re: [Wien] Segmentation fault in Supercell Calculation Your options are probably wrong: a) mpif90 is normally gfortran, the Intel version is mpiifort b) It is easy to use the wrong linking with the Intel mkl libraries. Please provide the information I requested. On Tue, Jul 28, 2015 at 2:55 PM, Lan, Wangwei mailto:wl...@my.fsu.edu>> wrote: Dear Professor: Yes, "x lapw0" works without mpi. My mpi compile : mpif90 I use Open MPI， version 1.4.5 the parallel compilation options are -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback -assume buffered_io I use Intel MKL libraries, that part should be fine. Thanks very much for your help. Sincerely Wangwei Lan From: wien-boun...@zeus.theochem.tuwien.ac.at<mailto:wien-boun...@zeus.theochem.tuwien.ac.at> mailto:wien-boun...@zeus.theochem.tuwien.ac.at>> on behalf of Laurence Marks mailto:l-ma...@northwestern.edu>> Sent: Tuesday, July 28, 2015 14:30 To: A Mailing list for WIEN2k users Subject: Re: [Wien] Segmentation fault in Supercell Calculation Does a simple "x lapw0" work, i.e. without mpi, for this specific case? If it does then there is probably an error in how you have linked/compiled the mpi versions. Please provide: a) The mpi compiler you used. b) Which type of mpi you are using (openmpi, mvapich, intel mpi etc) c) The parallel compilation options. N.B., a useful resource is https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor N.N.B., ulimit -s is not needed, this is (now) done in the software. On Tue, Jul 28, 2015 at 2:22 PM, Lan, Wangwei mailto:wl...@my.fsu.edu>> wrote: Dear Professor Marks: I've check everything you have mentioned, they are all fine, nevertheless it still don't work. I think the input files are ok since I have no problem running in non-parallel mode. I tried to make the supercell smaller (2x1x1), then it works. However, I don't know why that happens. By the way, I have "ulimit -s unlimited " in my .bashrc file. I'v also adjusted the RKMAX and RMT before. Sincerely Wangwei Lan From: wien-boun...@zeus.theochem.tuwien.ac.at<mailto:wien-boun...@zeus.theochem.tuwien.ac.at> mailto:wien-boun...@zeus.theochem.tuwien.ac.at>> on behalf of Laurence Marks mailto:l-ma...@northwestern.edu>> Sent: Tuesday, July 28, 2015 13:09 To: A Mailing list for WIEN2k users Subject: Re: [Wien] Segmentation fault in Supercell Calculation You have what is called a "Segmentation Violation" which was detected by 4 of the nodes and they called an error handler which stopped the mpi job on all the CPU's. This is normally because you have an error of some sort in your input files,
[Wien] crystal field splitting
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? I'v read several papers, they use wannier90 to calculate the on site energy, then interpret that on site energy difference as crystal field splitting. However, when I apply this method, I got controversy results as our group theory analysis. I seriously doubt about this kind of interpretation, hope you can help me. Thanks very much. Sincerely Wangwei Lan ___ 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] 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 on behalf of Víctor Luaña Cabal 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
[Wien] formation energy
Dear WIEN2k user: I am interested in the formation energy. I've searched the mailing address, but I still can't get it. I found the definition of formation energy is like this (Ga15MnN16 for example) : formation energy = total ENE of Ga15MnN16 -15*total ENE for Ga metal in standard state structure - 1* total ENE for Mn metal in standard state structure - 16* total ENE for N in standard structure In our system, it's TbOCl, does that mean: formation energy = = total ENE of TbOCl - tot ENE for Tb metal in standard state structure - tot ENE for O in standard state - Cl in standard state. ? If that is correct, what is the standard state structure for O and Cl? Do we need to do several other calculations for Tb metal or O standard state to get the formation energy? Thanks very much. Sincerely Wangwei Lan ___ 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] case.inkram energy shift
Dear WIEN2k user, I am now doing optical properties calculation for semimetals. I have a few question related to the energy shift in case.inkram file. If I don't do energy shift, I can't get a reasonable results compared to experiments. That brings me into two questions. First, what is energy shift here? How do you determine whether you need energy shift or not? Second,how do you determine the exact number of shift, is it shown in some file? Thanks in advance Sincerely Wangwei Lan ___ 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] xmgrace error
Dear WIEN2k User: I calculate the band structure in my case, and I can get the case.spaghetti_ps correctly. But when I want to use xmgrace to plot the band structure, it gives error show below. I am pretty sure WIEN2k works fine in my case. I searched the mailing list, but I can't find the answer for this problem. Does anyone have an idea on how to solve this problem? Thanks in advance. [Error] No valid graph selected: VIEW 0.12, 0.15, 0.90, 1.28 [Error] No valid axis selected: XAXIS LABEL CHAR SIZE 1.5 [Error] No valid axis selected: XAXIS TICKLABEL CHAR SIZE 1.25 [Error] No valid axis selected: YAXIS LABEL CHAR SIZE 1.5 [Error] No valid axis selected: YAXIS TICKLABEL CHAR SIZE 1.25 [Error] No valid axis selected: XAXIS TICK MAJOR GRID ON [Error] No valid axis selected: XAXIS TICK SPEC TYPE BOTH [Error] No valid axis selected: XAXIS TICK SPEC 11 [Error] No valid axis selected: XAXIS TICK MAJOR 0, 0.0 [Error] No valid axis selected: XAXIS TICKLABEL0 ,"GAM " [Error] No valid axis selected: XAXIS TICK MAJOR 1, 0.17980 [Error] No valid axis selected: XAXIS TICKLABEL1 ,"Z " [Error] No valid axis selected: XAXIS TICK MAJOR 2, 0.70609 [Error] No valid axis selected: XAXIS TICKLABEL2 ,"" [Error] No valid axis selected: XAXIS TICK MAJOR 3, 1.23783 [Error] No valid axis selected: XAXIS TICKLABEL3 ,"" [Error] No valid axis selected: XAXIS TICK MAJOR 4, 1.75455 [Error] No valid axis selected: XAXIS TICKLABEL4 ,"L1 " [Error] No valid axis selected: XAXIS TICK MAJOR 5, 2.13185 [Error] No valid axis selected: XAXIS TICKLABEL5 ,"B " [Error] No valid axis selected: XAXIS TICK MAJOR 6, 2.74100 [Error] No valid axis selected: XAXIS TICKLABEL6 ,"GAM " [Error] No valid axis selected: XAXIS TICK MAJOR 7, 3.26251 [Error] No valid axis selected: XAXIS TICKLABEL7 ,"L " [Error] No valid axis selected: XAXIS TICK MAJOR 8, 3.57160 [Error] No valid axis selected: XAXIS TICKLABEL8 ,"X " [Error] No valid axis selected: XAXIS TICK MAJOR 9, 4.18743 [Error] No valid axis selected: XAXIS TICKLABEL9 ,"" [Error] No valid axis selected: XAXIS TICK MAJOR 10, 4.78405 [Error] No valid axis selected: XAXIS TICKLABEL 10 ,"Q " Best regards Wangwei Lan ___ 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
