From nek5000-users at lists.mcs.anl.gov Sun Dec 1 01:06:14 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 1 Dec 2013 01:06:14 -0600 Subject: [Nek5000-users] nek+moab problem on mac osx 10.9 using macports In-Reply-To: References: Message-ID: Praveen, The linker with mpif77 cannot handle -stdlib since it should be passed to a clang compiler and not gfortran. Try changing the linker from mpif77 to mpicxx. I dont have a configuration setup with this combination of OpenMPI+clang to test currently. I have mpich3+clang3.4 on a ubuntu system and can try to check if NEK builds cleanly there after upgrading my gfortran. If there are clang issues, it should show up there too. Vijay On Sat, Nov 30, 2013 at 11:12 PM, wrote: > > On Sun, Dec 1, 2013 at 8:18 AM, wrote: >> >> AFAIK, these routines have not been deprecated in clang. Can you print >> out the version of your compilers so that we can see if some >> implementation is missing ? clang --version. >> >> You should also use LDFLAGS+="-stdlib=libstdc++" on the linker command >> since OSX Mavericks might have a different behavior by default in >> choosing the standard C++ runtime libraries. If that doesn't fix the >> undefined errors, let us know the detailed messages. >> >> Vijay > > > Hello Vijay > > Here is some information on my mpi which is installed from macports > > clang is from xcode. > > $ clang -v > > Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn) > > Target: x86_64-apple-darwin13.0.0 > > Thread model: posix > > > $ openmpicc -v > > Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn) > > Target: x86_64-apple-darwin13.0.0 > > Thread model: posix > > > $ openmpic++ -v > > Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn) > > Target: x86_64-apple-darwin13.0.0 > > Thread model: posix > > > $ openmpif77 -v > > Using built-in specs. > > COLLECT_GCC=/opt/local/bin/gfortran-mp-4.8 > > COLLECT_LTO_WRAPPER=/opt/local/libexec/gcc/x86_64-apple-darwin13/4.8.1/lto-wrapper > > Target: x86_64-apple-darwin13 > > Configured with: > /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc48/gcc48/work/gcc-4.8.1/configure > --prefix=/opt/local --build=x86_64-apple-darwin13 > --enable-languages=c,c++,objc,obj-c++,lto,fortran,java > --libdir=/opt/local/lib/gcc48 --includedir=/opt/local/include/gcc48 > --infodir=/opt/local/share/info --mandir=/opt/local/share/man > --datarootdir=/opt/local/share/gcc-4.8 --with-local-prefix=/opt/local > --with-system-zlib --disable-nls --program-suffix=-mp-4.8 > --with-gxx-include-dir=/opt/local/include/gcc48/c++/ --with-gmp=/opt/local > --with-mpfr=/opt/local --with-mpc=/opt/local --with-cloog=/opt/local > --enable-cloog-backend=isl --disable-cloog-version-check > --enable-stage1-checking --disable-multilib --enable-lto > --enable-libstdcxx-time --with-as=/opt/local/bin/as > --with-ld=/opt/local/bin/ld --with-ar=/opt/local/bin/ar > --with-bugurl=https://trac.macports.org/newticket > --with-pkgversion='MacPorts gcc48 4.8.1_3' > > Thread model: posix > > gcc version 4.8.1 (MacPorts gcc48 4.8.1_3) > > > I configure moab like this > > > ./configure --prefix=`pwd` \ > > --with-mpi \ > > --with-hdf5=/opt/local \ > > --enable-mbzoltan \ > > --with-zoltan=/opt/trilinos-11.4.1-mpi \ > > CC=openmpicc CXX=openmpic++ FC=openmpif77 F77=openmpif77 > > > If I add -stdlib=libstdc++ flag it is not recognized > > > makenek - automatic build tool for Nek5000 > > generating makefile ... > > openmpif77 -c -O2 -fdefault-real-8 -fdefault-double-8 -x f77-cpp-input > -fcray-pointer -DMOAB -DPTRSIZE8 -DMPI -DLONGINT8 -DUNDERSCORE > -DGLOBAL_LONG_LONG -I/Users/praveen/rayleigh3 > -I/Users/praveen/Applications/nek5_svn/trunk/nek -I./ > /Users/praveen/rayleigh3/ray.f > -I/Users/praveen/Applications/nek5_svn/trunk/nek/3rd_party > -I/Users/praveen/Applications/moab/moab-4.6.2/include -o obj/ray.o > > openmpif77 -o nek5000 obj/ray.o obj/drive.o obj/drive1.o obj/drive2.o > obj/plan4.o obj/bdry.o obj/coef.o obj/conduct.o obj/connect1.o > obj/connect2.o obj/dssum.o obj/edgec.o obj/eigsolv.o obj/gauss.o > obj/genxyz.o obj/navier1.o obj/makeq.o obj/navier0.o obj/navier2.o > obj/navier3.o obj/navier4.o obj/prepost.o obj/speclib.o obj/map2.o > obj/turb.o obj/mvmesh.o obj/ic.o obj/ssolv.o obj/planx.o obj/math.o > obj/mxm_wrapper.o obj/hmholtz.o obj/gfdm_par.o obj/gfdm_op.o > obj/gfdm_solve.o obj/subs1.o obj/subs2.o obj/genbox.o obj/gmres.o obj/hsmg.o > obj/convect.o obj/induct.o obj/perturb.o obj/navier5.o obj/navier6.o > obj/navier7.o obj/navier8.o obj/fast3d.o obj/fasts.o obj/calcz.o obj/byte.o > obj/chelpers.o obj/byte_mpi.o obj/postpro.o obj/cvode_driver.o > obj/nek_comm.o obj/init_plugin.o obj/setprop.o obj/qthermal.o > obj/cvode_aux.o obj/makeq_aux.o obj/papi.o obj/ssygv.o obj/dsygv.o > obj/nek_in_situ.o obj/mxm_std.o obj/blas.o obj/moab.o obj/imeshutil.o > obj/imeshcutil.o obj/comm_mpi.o obj/singlmesh.o obj/jl_gs.o obj/jl_sort.o > obj/jl_sarray_transfer.o obj/jl_sarray_sort.o obj/jl_gs_local.o > obj/jl_crystal.o obj/jl_comm.o obj/jl_tensor.o obj/jl_fail.o > obj/jl_fcrystal.o obj/jl_findpts.o obj/jl_findpts_local.o obj/jl_obbox.o > obj/jl_poly.o obj/jl_lob_bnd.o obj/jl_findpts_el_3.o obj/jl_findpts_el_2.o > obj/jl_sparse_cholesky.o obj/jl_xxt.o obj/jl_fcrs.o -L/opt/local/lib > -L/Users/praveen/Applications/moab/moab-4.6.2/lib > -L/Users/praveen/Applications/moab/moab-4.6.2/lib -liMesh -lMOAB -lnetcdf > -lhdf5 -lm -L/opt/local/lib > -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1 > -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1/../../.. -lmpi_usempi > -lmpi_mpifh -lmpi -lgfortran -lquadmath -lm -L/opt/local/lib > -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1 > -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1/../../.. -lmpi_usempi > -lmpi_mpifh -lmpi -lgfortran -lquadmath -lm -lmpi_cxx -lstdc++ > -stdlib=libstdc++ > > gfortran-mp-4.8: error: unrecognized command line option '-stdlib=libstdc++' > > make: *** [nek5000] Error 1 > > > Thanks > > praveen > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Sun Dec 1 01:24:05 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 1 Dec 2013 12:54:05 +0530 Subject: [Nek5000-users] nek+moab problem on mac osx 10.9 using macports In-Reply-To: References: Message-ID: On Sun, Dec 1, 2013 at 12:36 PM, wrote: > Praveen, > > The linker with mpif77 cannot handle -stdlib since it should be passed > to a clang compiler and not gfortran. Try changing the linker from > mpif77 to mpicxx. > > I dont have a configuration setup with this combination of > OpenMPI+clang to test currently. I have mpich3+clang3.4 on a ubuntu > system and can try to check if NEK builds cleanly there after > upgrading my gfortran. If there are clang issues, it should show up > there too. > > Vijay > Hello Vijay It seems that I have to use -stdlib=libc++ I manually changed the linker command in makefile. I dont get the c++ errors but something else openmpic++ -o nek5000 obj/ray.o obj/drive.o obj/drive1.o obj/drive2.o obj/plan4.o obj/bdry.o obj/coef.o obj/conduct.o obj/connect1.o obj/connect2.o obj/dssum.o obj/edgec.o obj/eigsolv.o obj/gauss.o obj/genxyz.o obj/navier1.o obj/makeq.o obj/navier0.o obj/navier2.o obj/navier3.o obj/navier4.o obj/prepost.o obj/speclib.o obj/map2.o obj/turb.o obj/mvmesh.o obj/ic.o obj/ssolv.o obj/planx.o obj/math.o obj/mxm_wrapper.o obj/hmholtz.o obj/gfdm_par.o obj/gfdm_op.o obj/gfdm_solve.o obj/subs1.o obj/subs2.o obj/genbox.o obj/gmres.o obj/hsmg.o obj/convect.o obj/induct.o obj/perturb.o obj/navier5.o obj/navier6.o obj/navier7.o obj/navier8.o obj/fast3d.o obj/fasts.o obj/calcz.o obj/byte.o obj/chelpers.o obj/byte_mpi.o obj/postpro.o obj/cvode_driver.o obj/nek_comm.o obj/init_plugin.o obj/setprop.o obj/qthermal.o obj/cvode_aux.o obj/makeq_aux.o obj/papi.o obj/ssygv.o obj/dsygv.o obj/nek_in_situ.o obj/mxm_std.o obj/blas.o obj/moab.o obj/imeshutil.o obj/imeshcutil.o obj/comm_mpi.o obj/singlmesh.o obj/jl_gs.o obj/jl_sort.o obj/jl_sarray_transfer.o obj/jl_sarray_sort.o obj/jl_gs_local.o obj/jl_crystal.o obj/jl_comm.o obj/jl_tensor.o obj/jl_fail.o obj/jl_fcrystal.o obj/jl_findpts.o obj/jl_findpts_local.o obj/jl_obbox.o obj/jl_poly.o obj/jl_lob_bnd.o obj/jl_findpts_el_3.o obj/jl_findpts_el_2.o obj/jl_sparse_cholesky.o obj/jl_xxt.o obj/jl_fcrs.o -L/opt/local/lib -L/Users/praveen/Applications/moab/moab-4.6.2/lib -L/Users/praveen/Applications/moab/moab-4.6.2/lib -liMesh -lMOAB -lnetcdf -lhdf5 -lm -L/opt/local/lib -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1 -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1/../../.. -lmpi_usempi -lmpi_mpifh -lmpi -lgfortran -lquadmath -lm -L/opt/local/lib -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1 -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1/../../.. -lmpi_usempi -lmpi_mpifh -lmpi -lgfortran -lquadmath -lm -lmpi_cxx -lstdc++ -stdlib=libc++ Undefined symbols for architecture x86_64: "_userq2_", referenced from: _setqvol_ in conduct.o _makeuq_ in conduct.o ld: symbol(s) not found for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [nek5000] Error 1 Thanks praveen -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sun Dec 1 01:38:51 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 1 Dec 2013 01:38:51 -0600 Subject: [Nek5000-users] nek+moab problem on mac osx 10.9 using macports In-Reply-To: References: Message-ID: > -stdlib=libc++ Ah I switched those around. But good that you figured this out. > Undefined symbols for architecture x86_64: > > "_userq2_", referenced from: userq2 should be part of your problem setup - *.usr file. Make sure this is defined and implemented correctly before appropriate linkage. On Sun, Dec 1, 2013 at 1:24 AM, wrote: > > On Sun, Dec 1, 2013 at 12:36 PM, wrote: >> >> Praveen, >> >> The linker with mpif77 cannot handle -stdlib since it should be passed >> to a clang compiler and not gfortran. Try changing the linker from >> mpif77 to mpicxx. >> >> I dont have a configuration setup with this combination of >> OpenMPI+clang to test currently. I have mpich3+clang3.4 on a ubuntu >> system and can try to check if NEK builds cleanly there after >> upgrading my gfortran. If there are clang issues, it should show up >> there too. >> >> Vijay > > > Hello Vijay > > It seems that I have to use > > -stdlib=libc++ > > I manually changed the linker command in makefile. I dont get the c++ errors > but something else > > openmpic++ -o nek5000 obj/ray.o obj/drive.o obj/drive1.o obj/drive2.o > obj/plan4.o obj/bdry.o obj/coef.o obj/conduct.o obj/connect1.o > obj/connect2.o obj/dssum.o obj/edgec.o obj/eigsolv.o obj/gauss.o > obj/genxyz.o obj/navier1.o obj/makeq.o obj/navier0.o obj/navier2.o > obj/navier3.o obj/navier4.o obj/prepost.o obj/speclib.o obj/map2.o > obj/turb.o obj/mvmesh.o obj/ic.o obj/ssolv.o obj/planx.o obj/math.o > obj/mxm_wrapper.o obj/hmholtz.o obj/gfdm_par.o obj/gfdm_op.o > obj/gfdm_solve.o obj/subs1.o obj/subs2.o obj/genbox.o obj/gmres.o obj/hsmg.o > obj/convect.o obj/induct.o obj/perturb.o obj/navier5.o obj/navier6.o > obj/navier7.o obj/navier8.o obj/fast3d.o obj/fasts.o obj/calcz.o obj/byte.o > obj/chelpers.o obj/byte_mpi.o obj/postpro.o obj/cvode_driver.o > obj/nek_comm.o obj/init_plugin.o obj/setprop.o obj/qthermal.o > obj/cvode_aux.o obj/makeq_aux.o obj/papi.o obj/ssygv.o obj/dsygv.o > obj/nek_in_situ.o obj/mxm_std.o obj/blas.o obj/moab.o obj/imeshutil.o > obj/imeshcutil.o obj/comm_mpi.o obj/singlmesh.o obj/jl_gs.o obj/jl_sort.o > obj/jl_sarray_transfer.o obj/jl_sarray_sort.o obj/jl_gs_local.o > obj/jl_crystal.o obj/jl_comm.o obj/jl_tensor.o obj/jl_fail.o > obj/jl_fcrystal.o obj/jl_findpts.o obj/jl_findpts_local.o obj/jl_obbox.o > obj/jl_poly.o obj/jl_lob_bnd.o obj/jl_findpts_el_3.o obj/jl_findpts_el_2.o > obj/jl_sparse_cholesky.o obj/jl_xxt.o obj/jl_fcrs.o -L/opt/local/lib > -L/Users/praveen/Applications/moab/moab-4.6.2/lib > -L/Users/praveen/Applications/moab/moab-4.6.2/lib -liMesh -lMOAB -lnetcdf > -lhdf5 -lm -L/opt/local/lib > -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1 > -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1/../../.. -lmpi_usempi > -lmpi_mpifh -lmpi -lgfortran -lquadmath -lm -L/opt/local/lib > -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1 > -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1/../../.. -lmpi_usempi > -lmpi_mpifh -lmpi -lgfortran -lquadmath -lm -lmpi_cxx -lstdc++ > -stdlib=libc++ > > Undefined symbols for architecture x86_64: > > "_userq2_", referenced from: > > _setqvol_ in conduct.o > > _makeuq_ in conduct.o > > ld: symbol(s) not found for architecture x86_64 > > clang: error: linker command failed with exit code 1 (use -v to see > invocation) > > make: *** [nek5000] Error 1 > > > Thanks > > praveen > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Sun Dec 1 01:56:40 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 1 Dec 2013 13:26:40 +0530 Subject: [Nek5000-users] nek+moab problem on mac osx 10.9 using macports In-Reply-To: References: Message-ID: Thanks. It compiles now. But I had to manually change the linker in the makefile generated by makenek. Is there a way to do this properly without having to edit makefile. Praveen On 1 Dec 2013 13:09, wrote: > > -stdlib=libc++ > > Ah I switched those around. But good that you figured this out. > > > Undefined symbols for architecture x86_64: > > > > "_userq2_", referenced from: > > userq2 should be part of your problem setup - *.usr file. Make sure > this is defined and implemented correctly before appropriate linkage. > > On Sun, Dec 1, 2013 at 1:24 AM, wrote: > > > > On Sun, Dec 1, 2013 at 12:36 PM, > wrote: > >> > >> Praveen, > >> > >> The linker with mpif77 cannot handle -stdlib since it should be passed > >> to a clang compiler and not gfortran. Try changing the linker from > >> mpif77 to mpicxx. > >> > >> I dont have a configuration setup with this combination of > >> OpenMPI+clang to test currently. I have mpich3+clang3.4 on a ubuntu > >> system and can try to check if NEK builds cleanly there after > >> upgrading my gfortran. If there are clang issues, it should show up > >> there too. > >> > >> Vijay > > > > > > Hello Vijay > > > > It seems that I have to use > > > > -stdlib=libc++ > > > > I manually changed the linker command in makefile. I dont get the c++ > errors > > but something else > > > > openmpic++ -o nek5000 obj/ray.o obj/drive.o obj/drive1.o obj/drive2.o > > obj/plan4.o obj/bdry.o obj/coef.o obj/conduct.o obj/connect1.o > > obj/connect2.o obj/dssum.o obj/edgec.o obj/eigsolv.o obj/gauss.o > > obj/genxyz.o obj/navier1.o obj/makeq.o obj/navier0.o obj/navier2.o > > obj/navier3.o obj/navier4.o obj/prepost.o obj/speclib.o obj/map2.o > > obj/turb.o obj/mvmesh.o obj/ic.o obj/ssolv.o obj/planx.o obj/math.o > > obj/mxm_wrapper.o obj/hmholtz.o obj/gfdm_par.o obj/gfdm_op.o > > obj/gfdm_solve.o obj/subs1.o obj/subs2.o obj/genbox.o obj/gmres.o > obj/hsmg.o > > obj/convect.o obj/induct.o obj/perturb.o obj/navier5.o obj/navier6.o > > obj/navier7.o obj/navier8.o obj/fast3d.o obj/fasts.o obj/calcz.o > obj/byte.o > > obj/chelpers.o obj/byte_mpi.o obj/postpro.o obj/cvode_driver.o > > obj/nek_comm.o obj/init_plugin.o obj/setprop.o obj/qthermal.o > > obj/cvode_aux.o obj/makeq_aux.o obj/papi.o obj/ssygv.o obj/dsygv.o > > obj/nek_in_situ.o obj/mxm_std.o obj/blas.o obj/moab.o obj/imeshutil.o > > obj/imeshcutil.o obj/comm_mpi.o obj/singlmesh.o obj/jl_gs.o obj/jl_sort.o > > obj/jl_sarray_transfer.o obj/jl_sarray_sort.o obj/jl_gs_local.o > > obj/jl_crystal.o obj/jl_comm.o obj/jl_tensor.o obj/jl_fail.o > > obj/jl_fcrystal.o obj/jl_findpts.o obj/jl_findpts_local.o obj/jl_obbox.o > > obj/jl_poly.o obj/jl_lob_bnd.o obj/jl_findpts_el_3.o > obj/jl_findpts_el_2.o > > obj/jl_sparse_cholesky.o obj/jl_xxt.o obj/jl_fcrs.o -L/opt/local/lib > > -L/Users/praveen/Applications/moab/moab-4.6.2/lib > > -L/Users/praveen/Applications/moab/moab-4.6.2/lib -liMesh -lMOAB -lnetcdf > > -lhdf5 -lm -L/opt/local/lib > > -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1 > > -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1/../../.. > -lmpi_usempi > > -lmpi_mpifh -lmpi -lgfortran -lquadmath -lm -L/opt/local/lib > > -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1 > > -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1/../../.. > -lmpi_usempi > > -lmpi_mpifh -lmpi -lgfortran -lquadmath -lm -lmpi_cxx -lstdc++ > > -stdlib=libc++ > > > > Undefined symbols for architecture x86_64: > > > > "_userq2_", referenced from: > > > > _setqvol_ in conduct.o > > > > _makeuq_ in conduct.o > > > > ld: symbol(s) not found for architecture x86_64 > > > > clang: error: linker command failed with exit code 1 (use -v to see > > invocation) > > > > make: *** [nek5000] Error 1 > > > > > > Thanks > > > > praveen > > > > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sun Dec 1 02:07:59 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 1 Dec 2013 02:07:59 -0600 Subject: [Nek5000-users] nek+moab problem on mac osx 10.9 using macports In-Reply-To: References: Message-ID: That should technically be an easy inclusion to NEK makenek script using say a LD variable to specify linker separate from compilers. But will leave that decision to the core NEK devs before I make any recommendations. Vijay On Sun, Dec 1, 2013 at 1:56 AM, wrote: > Thanks. It compiles now. But I had to manually change the linker in the > makefile generated by makenek. Is there a way to do this properly without > having to edit makefile. > > Praveen > > On 1 Dec 2013 13:09, wrote: >> >> > -stdlib=libc++ >> >> Ah I switched those around. But good that you figured this out. >> >> > Undefined symbols for architecture x86_64: >> > >> > "_userq2_", referenced from: >> >> userq2 should be part of your problem setup - *.usr file. Make sure >> this is defined and implemented correctly before appropriate linkage. >> >> On Sun, Dec 1, 2013 at 1:24 AM, wrote: >> > >> > On Sun, Dec 1, 2013 at 12:36 PM, >> > wrote: >> >> >> >> Praveen, >> >> >> >> The linker with mpif77 cannot handle -stdlib since it should be passed >> >> to a clang compiler and not gfortran. Try changing the linker from >> >> mpif77 to mpicxx. >> >> >> >> I dont have a configuration setup with this combination of >> >> OpenMPI+clang to test currently. I have mpich3+clang3.4 on a ubuntu >> >> system and can try to check if NEK builds cleanly there after >> >> upgrading my gfortran. If there are clang issues, it should show up >> >> there too. >> >> >> >> Vijay >> > >> > >> > Hello Vijay >> > >> > It seems that I have to use >> > >> > -stdlib=libc++ >> > >> > I manually changed the linker command in makefile. I dont get the c++ >> > errors >> > but something else >> > >> > openmpic++ -o nek5000 obj/ray.o obj/drive.o obj/drive1.o obj/drive2.o >> > obj/plan4.o obj/bdry.o obj/coef.o obj/conduct.o obj/connect1.o >> > obj/connect2.o obj/dssum.o obj/edgec.o obj/eigsolv.o obj/gauss.o >> > obj/genxyz.o obj/navier1.o obj/makeq.o obj/navier0.o obj/navier2.o >> > obj/navier3.o obj/navier4.o obj/prepost.o obj/speclib.o obj/map2.o >> > obj/turb.o obj/mvmesh.o obj/ic.o obj/ssolv.o obj/planx.o obj/math.o >> > obj/mxm_wrapper.o obj/hmholtz.o obj/gfdm_par.o obj/gfdm_op.o >> > obj/gfdm_solve.o obj/subs1.o obj/subs2.o obj/genbox.o obj/gmres.o >> > obj/hsmg.o >> > obj/convect.o obj/induct.o obj/perturb.o obj/navier5.o obj/navier6.o >> > obj/navier7.o obj/navier8.o obj/fast3d.o obj/fasts.o obj/calcz.o >> > obj/byte.o >> > obj/chelpers.o obj/byte_mpi.o obj/postpro.o obj/cvode_driver.o >> > obj/nek_comm.o obj/init_plugin.o obj/setprop.o obj/qthermal.o >> > obj/cvode_aux.o obj/makeq_aux.o obj/papi.o obj/ssygv.o obj/dsygv.o >> > obj/nek_in_situ.o obj/mxm_std.o obj/blas.o obj/moab.o obj/imeshutil.o >> > obj/imeshcutil.o obj/comm_mpi.o obj/singlmesh.o obj/jl_gs.o >> > obj/jl_sort.o >> > obj/jl_sarray_transfer.o obj/jl_sarray_sort.o obj/jl_gs_local.o >> > obj/jl_crystal.o obj/jl_comm.o obj/jl_tensor.o obj/jl_fail.o >> > obj/jl_fcrystal.o obj/jl_findpts.o obj/jl_findpts_local.o obj/jl_obbox.o >> > obj/jl_poly.o obj/jl_lob_bnd.o obj/jl_findpts_el_3.o >> > obj/jl_findpts_el_2.o >> > obj/jl_sparse_cholesky.o obj/jl_xxt.o obj/jl_fcrs.o -L/opt/local/lib >> > -L/Users/praveen/Applications/moab/moab-4.6.2/lib >> > -L/Users/praveen/Applications/moab/moab-4.6.2/lib -liMesh -lMOAB >> > -lnetcdf >> > -lhdf5 -lm -L/opt/local/lib >> > -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1 >> > -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1/../../.. >> > -lmpi_usempi >> > -lmpi_mpifh -lmpi -lgfortran -lquadmath -lm -L/opt/local/lib >> > -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1 >> > -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1/../../.. >> > -lmpi_usempi >> > -lmpi_mpifh -lmpi -lgfortran -lquadmath -lm -lmpi_cxx -lstdc++ >> > -stdlib=libc++ >> > >> > Undefined symbols for architecture x86_64: >> > >> > "_userq2_", referenced from: >> > >> > _setqvol_ in conduct.o >> > >> > _makeuq_ in conduct.o >> > >> > ld: symbol(s) not found for architecture x86_64 >> > >> > clang: error: linker command failed with exit code 1 (use -v to see >> > invocation) >> > >> > make: *** [nek5000] Error 1 >> > >> > >> > Thanks >> > >> > praveen >> > >> > >> > _______________________________________________ >> > Nek5000-users mailing list >> > Nek5000-users at lists.mcs.anl.gov >> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Sun Dec 1 07:59:15 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 1 Dec 2013 19:29:15 +0530 Subject: [Nek5000-users] Nekmoab does not work with pn/pn-2 In-Reply-To: References: Message-ID: Hello I could not use the pn/pn-2 spaces when reading mesh through moab which was generated by gmsh. I got a message that it is not supported. Is this a restriction with moab. Thanks Praveen -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sun Dec 1 10:56:44 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 1 Dec 2013 10:56:44 -0600 (CST) Subject: [Nek5000-users] Nekmoab does not work with pn/pn-2 In-Reply-To: Message-ID: Hi Praveen, The initial implementation of Nek-MOAB coupling was focused on 3D Pn-Pn cases -- what is the advantage of using Pn-Pn-2 formulation for you over Pn-Pn? Thanks. Aleks ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: "nek5000" Sent: Sunday, December 1, 2013 7:59:15 AM Subject: [Nek5000-users] Nekmoab does not work with pn/pn-2 Hello I could not use the pn/pn-2 spaces when reading mesh through moab which was generated by gmsh. I got a message that it is not supported. Is this a restriction with moab. Thanks Praveen _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Sun Dec 1 11:00:34 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 1 Dec 2013 11:00:34 -0600 (CST) Subject: [Nek5000-users] nek+moab problem on mac osx 10.9 using macports In-Reply-To: Message-ID: Thanks, Vijay and Praveen, Yes, userq2() is a part of Nek-MOAB interface -- see examples/moab_conjht/moab_conjht.usr I'll discuss the issue of linking with other developers. Best. Aleks ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: "nek5000-users" Sent: Sunday, December 1, 2013 2:07:59 AM Subject: Re: [Nek5000-users] nek+moab problem on mac osx 10.9 using macports That should technically be an easy inclusion to NEK makenek script using say a LD variable to specify linker separate from compilers. But will leave that decision to the core NEK devs before I make any recommendations. Vijay On Sun, Dec 1, 2013 at 1:56 AM, wrote: > Thanks. It compiles now. But I had to manually change the linker in the > makefile generated by makenek. Is there a way to do this properly without > having to edit makefile. > > Praveen > > On 1 Dec 2013 13:09, wrote: >> >> > -stdlib=libc++ >> >> Ah I switched those around. But good that you figured this out. >> >> > Undefined symbols for architecture x86_64: >> > >> > "_userq2_", referenced from: >> >> userq2 should be part of your problem setup - *.usr file. Make sure >> this is defined and implemented correctly before appropriate linkage. >> >> On Sun, Dec 1, 2013 at 1:24 AM, wrote: >> > >> > On Sun, Dec 1, 2013 at 12:36 PM, >> > wrote: >> >> >> >> Praveen, >> >> >> >> The linker with mpif77 cannot handle -stdlib since it should be passed >> >> to a clang compiler and not gfortran. Try changing the linker from >> >> mpif77 to mpicxx. >> >> >> >> I dont have a configuration setup with this combination of >> >> OpenMPI+clang to test currently. I have mpich3+clang3.4 on a ubuntu >> >> system and can try to check if NEK builds cleanly there after >> >> upgrading my gfortran. If there are clang issues, it should show up >> >> there too. >> >> >> >> Vijay >> > >> > >> > Hello Vijay >> > >> > It seems that I have to use >> > >> > -stdlib=libc++ >> > >> > I manually changed the linker command in makefile. I dont get the c++ >> > errors >> > but something else >> > >> > openmpic++ -o nek5000 obj/ray.o obj/drive.o obj/drive1.o obj/drive2.o >> > obj/plan4.o obj/bdry.o obj/coef.o obj/conduct.o obj/connect1.o >> > obj/connect2.o obj/dssum.o obj/edgec.o obj/eigsolv.o obj/gauss.o >> > obj/genxyz.o obj/navier1.o obj/makeq.o obj/navier0.o obj/navier2.o >> > obj/navier3.o obj/navier4.o obj/prepost.o obj/speclib.o obj/map2.o >> > obj/turb.o obj/mvmesh.o obj/ic.o obj/ssolv.o obj/planx.o obj/math.o >> > obj/mxm_wrapper.o obj/hmholtz.o obj/gfdm_par.o obj/gfdm_op.o >> > obj/gfdm_solve.o obj/subs1.o obj/subs2.o obj/genbox.o obj/gmres.o >> > obj/hsmg.o >> > obj/convect.o obj/induct.o obj/perturb.o obj/navier5.o obj/navier6.o >> > obj/navier7.o obj/navier8.o obj/fast3d.o obj/fasts.o obj/calcz.o >> > obj/byte.o >> > obj/chelpers.o obj/byte_mpi.o obj/postpro.o obj/cvode_driver.o >> > obj/nek_comm.o obj/init_plugin.o obj/setprop.o obj/qthermal.o >> > obj/cvode_aux.o obj/makeq_aux.o obj/papi.o obj/ssygv.o obj/dsygv.o >> > obj/nek_in_situ.o obj/mxm_std.o obj/blas.o obj/moab.o obj/imeshutil.o >> > obj/imeshcutil.o obj/comm_mpi.o obj/singlmesh.o obj/jl_gs.o >> > obj/jl_sort.o >> > obj/jl_sarray_transfer.o obj/jl_sarray_sort.o obj/jl_gs_local.o >> > obj/jl_crystal.o obj/jl_comm.o obj/jl_tensor.o obj/jl_fail.o >> > obj/jl_fcrystal.o obj/jl_findpts.o obj/jl_findpts_local.o obj/jl_obbox.o >> > obj/jl_poly.o obj/jl_lob_bnd.o obj/jl_findpts_el_3.o >> > obj/jl_findpts_el_2.o >> > obj/jl_sparse_cholesky.o obj/jl_xxt.o obj/jl_fcrs.o -L/opt/local/lib >> > -L/Users/praveen/Applications/moab/moab-4.6.2/lib >> > -L/Users/praveen/Applications/moab/moab-4.6.2/lib -liMesh -lMOAB >> > -lnetcdf >> > -lhdf5 -lm -L/opt/local/lib >> > -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1 >> > -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1/../../.. >> > -lmpi_usempi >> > -lmpi_mpifh -lmpi -lgfortran -lquadmath -lm -L/opt/local/lib >> > -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1 >> > -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1/../../.. >> > -lmpi_usempi >> > -lmpi_mpifh -lmpi -lgfortran -lquadmath -lm -lmpi_cxx -lstdc++ >> > -stdlib=libc++ >> > >> > Undefined symbols for architecture x86_64: >> > >> > "_userq2_", referenced from: >> > >> > _setqvol_ in conduct.o >> > >> > _makeuq_ in conduct.o >> > >> > ld: symbol(s) not found for architecture x86_64 >> > >> > clang: error: linker command failed with exit code 1 (use -v to see >> > invocation) >> > >> > make: *** [nek5000] Error 1 >> > >> > >> > Thanks >> > >> > praveen >> > >> > >> > _______________________________________________ >> > Nek5000-users mailing list >> > Nek5000-users at lists.mcs.anl.gov >> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Mon Dec 2 10:59:21 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 2 Dec 2013 22:29:21 +0530 Subject: [Nek5000-users] Nekmoab does not work with pn/pn-2 In-Reply-To: References: Message-ID: Hello I am solving variable viscosity problems using stress formulation which is available only for Pn/Pn-2. I have not tried the pn/pn for my problems and so dont have experience with it. Thanks Praveen On 1 Dec 2013 22:26, wrote: > Hi Praveen, > > The initial implementation of Nek-MOAB coupling was focused on 3D Pn-Pn > cases -- what is the advantage of using Pn-Pn-2 formulation for you over > Pn-Pn? > > Thanks. > Aleks > > ----- Original Message ----- > From: nek5000-users at lists.mcs.anl.gov > To: "nek5000" > Sent: Sunday, December 1, 2013 7:59:15 AM > Subject: [Nek5000-users] Nekmoab does not work with pn/pn-2 > > > > > Hello > I could not use the pn/pn-2 spaces when reading mesh through moab which > was generated by gmsh. I got a message that it is not supported. Is this a > restriction with moab. > Thanks > Praveen > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Dec 2 15:21:25 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 2 Dec 2013 21:21:25 +0000 Subject: [Nek5000-users] Turbulence DNS collaboration request Message-ID: Dear users, As a newcomer, I am delighted to discover that ANL has free downloads of DNS/LES f77 codes. I want to avail this opportunity because I have a very important and fundamental set of calculations to do regarding turbulent particle pair diffusion, for which I have developed a new theory that challenges Richardson's celebrated 1926 theory. However, I fear that the time I would to invest in learning to run and then analysing the vast data may be prohibitive for me. But fortunately, an opportunity by way of a possible research funding has arisen here in Saudi Arabia. I am about to submit an application along these lines, and I am allowed 1 or 2 international consultants on the project. This can also include periods of training for myself in USA ANL for example. There will be a compensation for the consultants involved. I am therefore requesting anyone interested who already knows how to run the an ANL spectral turbulent DNS code and is interested in this topic to kindly join me in this collaboration. We have large super computer in KAUST (the new university) and I believe that I can easily get access to it if needed. It has to be DNS, not LES. It must a spectral code for the purposes of testing my theory. It can be in 2D or 3D. (Or both cases.) It will involve creating a an algorithm for integrating the motion of passive particles to generate an ensemble of long particle trajectories, and hence to obtain Lagrangian particle pair statistics. This is in principle not difficult - I have a basic algorithm myself. The main problem is the sheer size of the data. I envisage about a 2 year project. I hope to produce at least 1 or 2 fundamental papers - and this will have something to say on the general theory of turbulence. My idea is essentially that pair diffusion in the inertial subrange is governed by both local and non-local correlations. Richardson and everyone else since then has assumed only local correlations are involved - at this moment I stand alone against the rest of the world! Alternatively, I could come to ANL to learn how to run and analyse the results - I would need someone, a 'consultant' in the project, at ANL to guide me for a few weeks. Is this possible? Please send me an email if you are interested. Thanks Nadeem Malik Professor Nadeem Malik, PhD(Cantab) Associate Professor King Fahd University of Petroleum and Minerals Department of Mathematics and Statistics P.O. Box 5046, Dhahran 31261, Kingdom of Saudi Arabia Tel: +966-3-860-7650 Email: namalik at kfupm.edu.sa Web: http://faculty.kfupm.edu.sa/math/namalik http://www.linkedin.com/in/nmalik11 Save a tree. Don't print this e-mail unless it's really necessary -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Dec 3 08:40:10 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 3 Dec 2013 15:40:10 +0100 Subject: [Nek5000-users] Vorticity in entire domain Message-ID: Dear Nek's I'm running the turbChannel case and trying to find the vorticity in the entire domain. With call comp_vort3(t(1,1,1,1,3),wo1,wo2,vx,vy,vz) I however get the 3 columns with length lx1*ly1*lz1*lelv. How do I make sure to gather the information from all processors? Any help would be greatly appreciated, Jurriaan -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Dec 3 08:47:06 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 3 Dec 2013 08:47:06 -0600 (CST) Subject: [Nek5000-users] Vorticity in entire domain In-Reply-To: References: Message-ID: Hi Jurriaan, Are you trying to compute a norm of the vorticity? Otherwise, vorticity is a vector field and can be viewed just like the velocity field, e.g. if (mod(istep,iostep).eq.0) $ call outpost(t(1,1,1,1,3),t(1,1,1,1,4),t(1,1,1,1,5),pr,t,'vrt') would create a set of files with vorticity in place of velocity. Paul On Tue, 3 Dec 2013, nek5000-users at lists.mcs.anl.gov wrote: > Dear Nek's > > I'm running the turbChannel case and trying to find the vorticity in the > entire domain. With > > call comp_vort3(t(1,1,1,1,3),wo1,wo2,vx,vy,vz) > > I however get the 3 columns with length lx1*ly1*lz1*lelv. How do I make > sure to gather the information from all processors? > Any help would be greatly appreciated, > > Jurriaan > From nek5000-users at lists.mcs.anl.gov Tue Dec 3 16:56:31 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 04 Dec 2013 00:56:31 +0200 Subject: [Nek5000-users] Vorticity in entire domain Message-ID: Dear Nek's I'm running the turbJet case and having the following runtime problem: Number of processors: 1 REAL wdsize : 8 INTEGER wdsize : 4 Beginning session: /home/galanti/COMPUTATION/NEK5000/nek5_svn/TEST-examples/turbJet/jet.rea timer accuracy: 0.0000000E+00 sec read .rea file read .re2 file byte swap: F 6.54321003 -2.93127722E+35 nelgt/nelgv/lelt: 9372 9372 1175 lx1 /lx2 /lx3 : 6 4 6 ABORT: Problem size too large! This solver has been compiled for: number of elements/proc (lelt): 1175 total number of elements (lelg): 10000 Recompile with the following SIZE parameters: lelt >= 9372 for np = 1 lelg >= 9372 call exitt: dying ... see full run.log in the attachment. Any one can help me how to control the size of the problem? Many thanks, Barak -------------- next part -------------- _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- A non-text attachment was scrubbed... Name: run.log Type: text/x-log Size: 2399 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Tue Dec 3 17:12:56 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 3 Dec 2013 16:12:56 -0700 Subject: [Nek5000-users] Vorticity in entire domain In-Reply-To: References: Message-ID: Hi Barak, please check for your nelx, nely and nelz. Your lelg greater than or equal to nelx*nely*nelz. Also, check for lelt,lelv, greater than or equal to lelg/np. Go to the SIZE file and make the changes. If you use lelg = 10,000, lelt = 1175, you must use np > 8 (appx 9) for your problem. Thanks, Tanmoy On Tue, Dec 3, 2013 at 3:56 PM, wrote: > Dear Nek's > > I'm running the turbJet case and having the following runtime problem: > > Number of processors: 1 > REAL wdsize : 8 > INTEGER wdsize : 4 > > > Beginning session: > /home/galanti/COMPUTATION/NEK5000/nek5_svn/TEST-examples/turbJet/jet.rea > > > timer accuracy: 0.0000000E+00 sec > > read .rea file > read .re2 file > byte swap: F 6.54321003 -2.93127722E+35 > nelgt/nelgv/lelt: 9372 9372 1175 > lx1 /lx2 /lx3 : 6 4 6 > > > ABORT: Problem size too large! > > This solver has been compiled for: > number of elements/proc (lelt): 1175 > total number of elements (lelg): 10000 > > Recompile with the following SIZE parameters: > lelt >= 9372 for np = 1 > lelg >= 9372 > > > call exitt: dying ... > > > see full run.log in the attachment. > Any one can help me how to control the size of the problem? > Many thanks, > Barak > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Dec 4 11:41:49 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 4 Dec 2013 12:41:49 -0500 Subject: [Nek5000-users] nhis Message-ID: " Mime-Version: 1.0 (Mac OS X Mail 7.0 \(1822\)) X-Mailer: Apple Mail (2.1822) Hi, I would like to extract the time-averaged values from a avgcase0.f00001 file of, for example, the velocity components at some specific locations. To do that, i set nek5000 in "post-processing mode? by setting nsteps=0, read the file in the userchck and call hpts(). I need a large number of locations I want to interpolate at (stored in hpts.in), much larger than the default nhis=100 in SIZE. I am finding spurious values in the hpts.out file at some locations. These spurious values and their locations change when I change nhis. I am doing something wrong?. There is a better way to do that?. Thanks. From nek5000-users at lists.mcs.anl.gov Wed Dec 4 08:00:53 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 4 Dec 2013 15:00:53 +0100 Subject: [Nek5000-users] Vorticity in entire domain Message-ID: Thank you, Paul. This was what I needed. Kind regards, Jurriaan -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Dec 4 15:11:29 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 4 Dec 2013 15:11:29 -0600 Subject: [Nek5000-users] nhis In-Reply-To: References: Message-ID: Hi, nhis in SIZE is the number of points, per processor, that can be read in. So, you will want to be sure that the total number of points in hpts.in = nhis*np. If this is the case and you are still getting strange values in hpts.out, we can look at other possible problems. Thanks Katie On Wed, Dec 4, 2013 at 11:41 AM, wrote: > " > Mime-Version: 1.0 (Mac OS X Mail 7.0 \(1822\)) > X-Mailer: Apple Mail (2.1822) > > Hi, > > I would like to extract the time-averaged values from a avgcase0.f00001 > file of, for example, the velocity components at some specific locations. > > To do that, i set nek5000 in "post-processing mode? by setting nsteps=0, > read the file in the userchck and call hpts(). > I need a large number of locations I want to interpolate at (stored in > hpts.in), much larger than the default nhis=100 in SIZE. > I am finding spurious values in the hpts.out file at some locations. These > spurious values and their locations change when I change nhis. > > I am doing something wrong?. There is a better way to do that?. > > Thanks. > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Dec 5 08:17:40 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 5 Dec 2013 14:17:40 +0000 Subject: [Nek5000-users] nhis In-Reply-To: References: Message-ID: Hi, so hpts.in = nhis*np or hpts.in <= nhis*np? Thanks On Dec 4, 2013, at 4:11 PM, > > wrote: Hi, nhis in SIZE is the number of points, per processor, that can be read in. So, you will want to be sure that the total number of points in hpts.in = nhis*np. If this is the case and you are still getting strange values in hpts.out, we can look at other possible problems. Thanks Katie On Wed, Dec 4, 2013 at 11:41 AM, > wrote: " > Mime-Version: 1.0 (Mac OS X Mail 7.0 \(1822\)) X-Mailer: Apple Mail (2.1822) Hi, I would like to extract the time-averaged values from a avgcase0.f00001 file of, for example, the velocity components at some specific locations. To do that, i set nek5000 in "post-processing mode? by setting nsteps=0, read the file in the userchck and call hpts(). I need a large number of locations I want to interpolate at (stored in hpts.in), much larger than the default nhis=100 in SIZE. I am finding spurious values in the hpts.out file at some locations. These spurious values and their locations change when I change nhis. I am doing something wrong?. There is a better way to do that?. Thanks. _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users ________________________________ CSI has been ranked one of America?s Best Colleges 2014 (North East Public) by US News and World Report. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Dec 5 09:29:51 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 5 Dec 2013 09:29:51 -0600 (CST) Subject: [Nek5000-users] nhis In-Reply-To: References: Message-ID: <= On Thu, 5 Dec 2013, nek5000-users at lists.mcs.anl.gov wrote: > Hi, > > so hpts.in = nhis*np or hpts.in <= nhis*np? > > Thanks > > > On Dec 4, 2013, at 4:11 PM, > > wrote: > > Hi, > > nhis in SIZE is the number of points, per processor, that can be read in. So, you will want to be sure that the total number of points in hpts.in = nhis*np. > > If this is the case and you are still getting strange values in hpts.out, we can look at other possible problems. > > Thanks > Katie > > > On Wed, Dec 4, 2013 at 11:41 AM, > wrote: > " > > Mime-Version: 1.0 (Mac OS X Mail 7.0 \(1822\)) > X-Mailer: Apple Mail (2.1822) > > Hi, > > I would like to extract the time-averaged values from a avgcase0.f00001 file of, for example, the velocity components at some specific locations. > > To do that, i set nek5000 in "post-processing mode? by setting nsteps=0, read the file in the userchck and call hpts(). > I need a large number of locations I want to interpolate at (stored in hpts.in), much larger than the default nhis=100 in SIZE. > I am finding spurious values in the hpts.out file at some locations. These spurious values and their locations change when I change nhis. > > I am doing something wrong?. There is a better way to do that?. > > Thanks. > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > ________________________________ > > CSI has been ranked one of America?s Best Colleges 2014 (North East Public) by US News and World Report. > From nek5000-users at lists.mcs.anl.gov Thu Dec 5 13:16:35 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 5 Dec 2013 11:16:35 -0800 Subject: [Nek5000-users] nhis Message-ID: Hi, I have found that if you set lhis to npts/np you get data that's messed up and out of order, BUT if you set lhis to npts it works fine. I think there is a bug in hpts (see my email to the users group on Nov 13 and copied below). However, I have some pretty big grids, so I need to use the parallelization feature (i.e., set lhis to npts/np, here npts = total number of interpolation points and np =number of processors). However, then the data output to hpts.out is jumbled up. If I instead set lhis to the total number of points, the output data is fine. I suspect there is a bug somewhere in hpts such that it mixes up the data. Cheers, Janet ------------------------------ > > Message: 3 > Date: Wed, 4 Dec 2013 15:11:29 -0600 > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] nhis > Message-ID: > > Content-Type: text/plain; charset="windows-1252" > > Hi, > > nhis in SIZE is the number of points, per processor, that can be read in. > So, you will want to be sure that the total number of points in hpts.in = > nhis*np. > > If this is the case and you are still getting strange values in hpts.out, > we can look at other possible problems. > > Thanks > Katie > > > On Wed, Dec 4, 2013 at 11:41 AM, wrote: > > > " > > Mime-Version: 1.0 (Mac OS X Mail 7.0 \(1822\)) > > X-Mailer: Apple Mail (2.1822) > > > > Hi, > > > > I would like to extract the time-averaged values from a avgcase0.f00001 > > file of, for example, the velocity components at some specific locations. > > > > To do that, i set nek5000 in "post-processing mode? by setting nsteps=0, > > read the file in the userchck and call hpts(). > > I need a large number of locations I want to interpolate at (stored in > > hpts.in), much larger than the default nhis=100 in SIZE. > > I am finding spurious values in the hpts.out file at some locations. > These > > spurious values and their locations change when I change nhis. > > > > I am doing something wrong?. There is a better way to do that?. > > > > Thanks. > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -- Janet Scheel Assistant Professor of Physics Occidental College 1600 Campus Road, M21 Los Angeles, CA 90041 (323) 259-2777 jscheel at oxy.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Dec 5 15:23:03 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 5 Dec 2013 16:23:03 -0500 Subject: [Nek5000-users] nhis In-Reply-To: References: Message-ID: Hi, yes, after setting nhis=npts (number of locations in hpts.in) instead of nhis=>npts/nproc, the results in hpts.out where what I expected, no ?messed up? values. Thanks. On Dec 5, 2013, at 2:16 PM, nek5000-users at lists.mcs.anl.gov wrote: > > Hi, > > I have found that if you set lhis to npts/np you get data that's messed up and out of order, BUT if you set lhis to npts it works fine. I think there is a bug in hpts (see my email to the users group on Nov 13 and copied below). > > > However, I have some pretty big grids, so I need to use the parallelization feature (i.e., set lhis to npts/np, here npts = total number of interpolation > points and np =number of processors). However, then the data output to hpts.out is jumbled up. If I instead set lhis to the total number of points, the output data is > fine. I suspect there is a bug somewhere in hpts such that it mixes up the data. > > Cheers, > > Janet > > > > ------------------------------ > > Message: 3 > Date: Wed, 4 Dec 2013 15:11:29 -0600 > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] nhis > Message-ID: > > Content-Type: text/plain; charset="windows-1252" > > Hi, > > nhis in SIZE is the number of points, per processor, that can be read in. > So, you will want to be sure that the total number of points in hpts.in = > nhis*np. > > If this is the case and you are still getting strange values in hpts.out, > we can look at other possible problems. > > Thanks > Katie > > > On Wed, Dec 4, 2013 at 11:41 AM, wrote: > > > " > > Mime-Version: 1.0 (Mac OS X Mail 7.0 \(1822\)) > > X-Mailer: Apple Mail (2.1822) > > > > Hi, > > > > I would like to extract the time-averaged values from a avgcase0.f00001 > > file of, for example, the velocity components at some specific locations. > > > > To do that, i set nek5000 in "post-processing mode? by setting nsteps=0, > > read the file in the userchck and call hpts(). > > I need a large number of locations I want to interpolate at (stored in > > hpts.in), much larger than the default nhis=100 in SIZE. > > I am finding spurious values in the hpts.out file at some locations. These > > spurious values and their locations change when I change nhis. > > > > I am doing something wrong?. There is a better way to do that?. > > > > Thanks. > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > > -- > Janet Scheel > Assistant Professor of Physics > Occidental College > 1600 Campus Road, M21 > Los Angeles, CA 90041 > (323) 259-2777 > jscheel at oxy.edu > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Dec 6 16:31:51 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 07 Dec 2013 00:31:51 +0200 Subject: [Nek5000-users] turbJet problem In-Reply-To: References: Message-ID: Hello, I am testing the example turbJet, and it seems that I have some problem with output. This are the output files: jet0.f00001 Moreover, the ran stops with emergency exit at time 5.64 (CFL too large?): 282 DNORM, DIVEX 6.2789891850172769E-004 8.4967723454134898E-006 282 5.6400E+00 1.1065E+01 Fluid done 282 5.6400000E+00 1.1955953E-03 6.4269380E-04 9.9999991E-01 e2 t max/min: 0.0000000000000000 0.0000000000000000 CFL, Ctarg! 22.504301079496056 2.0000000000000000 call outfld: ifpsco: T 283 5.6400E+00 Write checkpoint: 0 283 OPEN: jet0.f00001 283 5.6400E+00 done :: Write checkpoint file size = 55. MB avg data-throughput = 572.1MB/s io-nodes = 1 7 Emergency exit: 283 time = 5.6399999999999677 Latest solution and data are dumped for post-processing. *** STOP *** 3 Emergency exit: 283 time = 5.6399999999999677 Latest solution and data are dumped for post-processing. *** STOP *** 5 Emergency exit: 283 time = 5.6399999999999677 Latest solution and data are dumped for post-processing. *** STOP *** 0 Emergency exit: 283 time = 5.6399999999999677 Latest solution and data are dumped for post-processing. *** STOP *** 6 Emergency exit: 283 time = 5.6399999999999677 Latest solution and data are dumped for post-processing. *** STOP *** 4 Emergency exit: 283 time = 5.6399999999999677 Latest solution and data are dumped for post-processing. *** STOP *** 2 Emergency exit: 283 time = 5.6399999999999677 Latest solution and data are dumped for post-processing. *** STOP *** 1 Emergency exit: 283 time = 5.6399999999999677 Thank you, Barak From nek5000-users at lists.mcs.anl.gov Fri Dec 6 16:42:46 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 6 Dec 2013 15:42:46 -0700 Subject: [Nek5000-users] turbJet problem In-Reply-To: References: Message-ID: Hi Barak, It is a problem with numerical Stability. Decrease DT in your .rea file until the simulations become stable. You could start with 1/2 DT to check if simulation is stable, other wise go for 1/4 DT, and check with this simple test. Thanks, Tanmoy On Fri, Dec 6, 2013 at 3:31 PM, wrote: > Hello, > I am testing the example turbJet, and it seems that I have some problem > with output. This are the output files: > jet0.f00001 > > Moreover, the ran stops with emergency exit at time 5.64 (CFL too large?): > > > 282 DNORM, DIVEX 6.2789891850172769E-004 8.4967723454134898E-006 > 282 5.6400E+00 1.1065E+01 Fluid done > 282 5.6400000E+00 1.1955953E-03 6.4269380E-04 9.9999991E-01 e2 > t max/min: 0.0000000000000000 0.0000000000000000 > CFL, Ctarg! 22.504301079496056 2.0000000000000000 > call outfld: ifpsco: T > > 283 5.6400E+00 Write checkpoint: > 0 283 OPEN: jet0.f00001 > > 283 5.6400E+00 done :: Write checkpoint > file size = 55. MB > avg data-throughput = 572.1MB/s > io-nodes = 1 > > > 7 Emergency exit: 283 time = 5.6399999999999677 > Latest solution and data are dumped for post-processing. > *** STOP *** > 3 Emergency exit: 283 time = 5.6399999999999677 > Latest solution and data are dumped for post-processing. > *** STOP *** > 5 Emergency exit: 283 time = 5.6399999999999677 > Latest solution and data are dumped for post-processing. > *** STOP *** > 0 Emergency exit: 283 time = 5.6399999999999677 > Latest solution and data are dumped for post-processing. > *** STOP *** > 6 Emergency exit: 283 time = 5.6399999999999677 > Latest solution and data are dumped for post-processing. > *** STOP *** > 4 Emergency exit: 283 time = 5.6399999999999677 > Latest solution and data are dumped for post-processing. > *** STOP *** > 2 Emergency exit: 283 time = 5.6399999999999677 > Latest solution and data are dumped for post-processing. > *** STOP *** > 1 Emergency exit: 283 time = 5.6399999999999677 > > > > > Thank you, > Barak > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sat Dec 7 11:33:27 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 07 Dec 2013 19:33:27 +0200 Subject: [Nek5000-users] turbJet problem In-Reply-To: References: Message-ID: Hi Tanmoy, Many thanks. It seems that after dividing by 4 (dt=0.005) it runs and I get output files in the form jet0.fxxxxx . Now I am trying to visualize them using the precompiled ubuntu11 version of visit. Unfortunately, I get the following error: VisIt could not read from the file "/home/galanti/COMPUTATION/NEK5000/nek5_svn/TEST-examples/turbJet/jet0.f* database". The generated error message was: There was an error opening /home/galanti/COMPUTATION/NEK5000/nek5_svn/TEST-examples/turbJet/jet0.f* database. It may be an invalid file. VisIt tried using the following file format readers to open the file: Nek5000 The following error(s) may be helpful in identifying the problem: When attempting to use "Nek", the file matched the general format expected by the reader but eventually encountered this error: "A tag called filetemplate: must be specified". What's wrong? Many thanks again, Barak On 12/07/2013 12:42 AM, nek5000-users at lists.mcs.anl.gov wrote: > Hi Barak, > > It is a problem with numerical Stability. Decrease DT in your .rea file > until the simulations become stable. You could start with 1/2 DT to > check if simulation is stable, other wise go for 1/4 DT, and check with > this simple test. > > Thanks, > Tanmoy > > > On Fri, Dec 6, 2013 at 3:31 PM, > wrote: > > Hello, > I am testing the example turbJet, and it seems that I have some > problem with output. This are the output files: > jet0.f00001 > > Moreover, the ran stops with emergency exit at time 5.64 (CFL too > large?): > > > 282 DNORM, DIVEX 6.2789891850172769E-004 > 8.4967723454134898E-006 > 282 5.6400E+00 1.1065E+01 Fluid done > 282 5.6400000E+00 1.1955953E-03 6.4269380E-04 9.9999991E-01 e2 > t max/min: 0.0000000000000000 0.0000000000000000 > CFL, Ctarg! 22.504301079496056 2.0000000000000000 > call outfld: ifpsco: T > > 283 5.6400E+00 Write checkpoint: > 0 283 OPEN: jet0.f00001 > > 283 5.6400E+00 done :: Write checkpoint > file size = 55. MB > avg data-throughput = 572.1MB/s > io-nodes = 1 > > > 7 Emergency exit: 283 time = > 5.6399999999999677 > Latest solution and data are dumped for post-processing. > *** STOP *** > 3 Emergency exit: 283 time = > 5.6399999999999677 > Latest solution and data are dumped for post-processing. > *** STOP *** > 5 Emergency exit: 283 time = > 5.6399999999999677 > Latest solution and data are dumped for post-processing. > *** STOP *** > 0 Emergency exit: 283 time = > 5.6399999999999677 > Latest solution and data are dumped for post-processing. > *** STOP *** > 6 Emergency exit: 283 time = > 5.6399999999999677 > Latest solution and data are dumped for post-processing. > *** STOP *** > 4 Emergency exit: 283 time = > 5.6399999999999677 > Latest solution and data are dumped for post-processing. > *** STOP *** > 2 Emergency exit: 283 time = > 5.6399999999999677 > Latest solution and data are dumped for post-processing. > *** STOP *** > 1 Emergency exit: 283 time = > 5.6399999999999677 > > > > > Thank you, > Barak > > > _________________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.__gov > > https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users > > > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Sat Dec 7 12:37:17 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 7 Dec 2013 11:37:17 -0700 Subject: [Nek5000-users] turbJet problem In-Reply-To: References: Message-ID: Hi Barak, it is because of the fact that the generated file format is probably not readable in visit. In the *usrchk* subroutine in your .usr file write these 2 lines param(66) = 4 param(67) = 4 before the end of the routine Then compile and execute your program. Now you will get output files in the form of turbJet.fld001, turbJet.fld002, ...and so on. type in visnek turbJet in your terminal, and generate *turbJet.nek5000*. This .nek5000 file can be read by visit. Thanks, Tanmoy On Sat, Dec 7, 2013 at 10:33 AM, wrote: > Hi Tanmoy, > Many thanks. It seems that after dividing by 4 (dt=0.005) it runs and I > get output files in the form jet0.fxxxxx . > Now I am trying to visualize them using the precompiled ubuntu11 version > of visit. Unfortunately, I get the following error: > > VisIt could not read from the file "/home/galanti/COMPUTATION/ > NEK5000/nek5_svn/TEST-examples/turbJet/jet0.f* database". > > The generated error message was: > > There was an error opening /home/galanti/COMPUTATION/ > NEK5000/nek5_svn/TEST-examples/turbJet/jet0.f* database. It may be an > invalid file. VisIt tried using the following file format readers to open > the file: Nek5000 > > The following error(s) may be helpful in identifying the problem: > When attempting to use "Nek", the file matched the general format expected > by the reader but eventually encountered this error: "A tag called > filetemplate: must be specified". > > What's wrong? > Many thanks again, > Barak > > > > On 12/07/2013 12:42 AM, nek5000-users at lists.mcs.anl.gov wrote: > >> Hi Barak, >> >> It is a problem with numerical Stability. Decrease DT in your .rea file >> until the simulations become stable. You could start with 1/2 DT to >> check if simulation is stable, other wise go for 1/4 DT, and check with >> this simple test. >> >> Thanks, >> Tanmoy >> >> >> On Fri, Dec 6, 2013 at 3:31 PM, > > wrote: >> >> Hello, >> I am testing the example turbJet, and it seems that I have some >> problem with output. This are the output files: >> jet0.f00001 >> >> Moreover, the ran stops with emergency exit at time 5.64 (CFL too >> large?): >> >> >> 282 DNORM, DIVEX 6.2789891850172769E-004 >> 8.4967723454134898E-006 >> 282 5.6400E+00 1.1065E+01 Fluid done >> 282 5.6400000E+00 1.1955953E-03 6.4269380E-04 9.9999991E-01 e2 >> t max/min: 0.0000000000000000 0.0000000000000000 >> CFL, Ctarg! 22.504301079496056 2.0000000000000000 >> call outfld: ifpsco: T >> >> 283 5.6400E+00 Write checkpoint: >> 0 283 OPEN: jet0.f00001 >> >> 283 5.6400E+00 done :: Write checkpoint >> file size = 55. MB >> avg data-throughput = 572.1MB/s >> io-nodes = 1 >> >> >> 7 Emergency exit: 283 time = >> 5.6399999999999677 >> Latest solution and data are dumped for post-processing. >> *** STOP *** >> 3 Emergency exit: 283 time = >> 5.6399999999999677 >> Latest solution and data are dumped for post-processing. >> *** STOP *** >> 5 Emergency exit: 283 time = >> 5.6399999999999677 >> Latest solution and data are dumped for post-processing. >> *** STOP *** >> 0 Emergency exit: 283 time = >> 5.6399999999999677 >> Latest solution and data are dumped for post-processing. >> *** STOP *** >> 6 Emergency exit: 283 time = >> 5.6399999999999677 >> Latest solution and data are dumped for post-processing. >> *** STOP *** >> 4 Emergency exit: 283 time = >> 5.6399999999999677 >> Latest solution and data are dumped for post-processing. >> *** STOP *** >> 2 Emergency exit: 283 time = >> 5.6399999999999677 >> Latest solution and data are dumped for post-processing. >> *** STOP *** >> 1 Emergency exit: 283 time = >> 5.6399999999999677 >> >> >> >> >> Thank you, >> Barak >> >> >> _________________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.__gov >> >> https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users >> >> >> >> >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sun Dec 8 13:26:55 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 08 Dec 2013 21:26:55 +0200 Subject: [Nek5000-users] turbJet problem In-Reply-To: References: Message-ID: Hi Tanmoy, I have divided by 4 and again my run stopped at iteration 1200. My question is: does nek5000 have variable time-stepping? Thanks, Barak On 12/07/2013 08:37 PM, nek5000-users at lists.mcs.anl.gov wrote: > Hi Barak, > > it is because of the fact that the generated file format is probably not > readable in visit. In the *usrchk* subroutine in your .usr file write > these 2 lines > param(66) = 4 > param(67) = 4 > > before the end of the routine > > Then compile and execute your program. Now you will get output files in > the form of turbJet.fld001, turbJet.fld002, ...and so on. > type in visnek turbJet in your terminal, and generate *turbJet.nek5000*. > This .nek5000 file can be read by visit. > > Thanks, > Tanmoy > > > On Sat, Dec 7, 2013 at 10:33 AM, > wrote: > > Hi Tanmoy, > Many thanks. It seems that after dividing by 4 (dt=0.005) it runs > and I get output files in the form jet0.fxxxxx . > Now I am trying to visualize them using the precompiled ubuntu11 > version of visit. Unfortunately, I get the following error: > > VisIt could not read from the file > "/home/galanti/COMPUTATION/__NEK5000/nek5_svn/TEST-__examples/turbJet/jet0.f* > database". > > The generated error message was: > > There was an error opening > /home/galanti/COMPUTATION/__NEK5000/nek5_svn/TEST-__examples/turbJet/jet0.f* > database. It may be an invalid file. VisIt tried using the > following file format readers to open the file: Nek5000 > > The following error(s) may be helpful in identifying the problem: > When attempting to use "Nek", the file matched the general format > expected by the reader but eventually encountered this error: "A tag > called filetemplate: must be specified". > > What's wrong? > Many thanks again, > Barak > > > > On 12/07/2013 12:42 AM, nek5000-users at lists.mcs.anl.__gov > wrote: > > Hi Barak, > > It is a problem with numerical Stability. Decrease DT in your > .rea file > until the simulations become stable. You could start with 1/2 DT to > check if simulation is stable, other wise go for 1/4 DT, and > check with > this simple test. > > Thanks, > Tanmoy > > > On Fri, Dec 6, 2013 at 3:31 PM, > > >> wrote: > > Hello, > I am testing the example turbJet, and it seems that I have some > problem with output. This are the output files: > jet0.f00001 > > Moreover, the ran stops with emergency exit at time 5.64 > (CFL too > large?): > > > 282 DNORM, DIVEX 6.2789891850172769E-004 > 8.4967723454134898E-006 > 282 5.6400E+00 1.1065E+01 Fluid done > 282 5.6400000E+00 1.1955953E-03 6.4269380E-04 > 9.9999991E-01 e2 > t max/min: 0.0000000000000000 0.0000000000000000 > CFL, Ctarg! 22.504301079496056 2.0000000000000000 > call outfld: ifpsco: T > > 283 5.6400E+00 Write checkpoint: > 0 283 OPEN: jet0.f00001 > > 283 5.6400E+00 done :: Write checkpoint > file size = 55. MB > avg data-throughput = > 572.1MB/s > io-nodes = 1 > > > 7 Emergency exit: 283 time = > 5.6399999999999677 > Latest solution and data are dumped for post-processing. > *** STOP *** > 3 Emergency exit: 283 time = > 5.6399999999999677 > Latest solution and data are dumped for post-processing. > *** STOP *** > 5 Emergency exit: 283 time = > 5.6399999999999677 > Latest solution and data are dumped for post-processing. > *** STOP *** > 0 Emergency exit: 283 time = > 5.6399999999999677 > Latest solution and data are dumped for post-processing. > *** STOP *** > 6 Emergency exit: 283 time = > 5.6399999999999677 > Latest solution and data are dumped for post-processing. > *** STOP *** > 4 Emergency exit: 283 time = > 5.6399999999999677 > Latest solution and data are dumped for post-processing. > *** STOP *** > 2 Emergency exit: 283 time = > 5.6399999999999677 > Latest solution and data are dumped for post-processing. > *** STOP *** > 1 Emergency exit: 283 time = > 5.6399999999999677 > > > > > Thank you, > Barak > > > ___________________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.____gov > > > https://lists.mcs.anl.gov/____mailman/listinfo/nek5000-users > > __> > > > > > > _________________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.__gov > > https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users > > > > _________________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.__gov > > https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users > > > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Sun Dec 8 18:56:56 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 8 Dec 2013 17:56:56 -0700 Subject: [Nek5000-users] turbJet problem In-Reply-To: References: Message-ID: Hi Barak, I am not aware of variable time stepping in nek5000. The time stepping used is BDFk/EXTk with CFL constraint for stability. You can change TORDER in .rea file to 2 or 3 to make the time stepping 2nd or third order accurate. There is a characteristic based time-stepping though... IFCHAR in .rea file. However, if for a value ot DT you are getting convergence, essentially you should get the same for smaller value of DT. What is the error you are getting after the program aborts after 1200 iterations? It is still stored in your log file I suppose. Thanks, Tanmoy On Sun, Dec 8, 2013 at 12:26 PM, wrote: > Hi Tanmoy, > I have divided by 4 and again my run stopped at iteration 1200. My > question is: does nek5000 have variable time-stepping? > Thanks, > Barak > > > On 12/07/2013 08:37 PM, nek5000-users at lists.mcs.anl.gov wrote: > >> Hi Barak, >> >> it is because of the fact that the generated file format is probably not >> readable in visit. In the *usrchk* subroutine in your .usr file write >> >> these 2 lines >> param(66) = 4 >> param(67) = 4 >> >> before the end of the routine >> >> Then compile and execute your program. Now you will get output files in >> the form of turbJet.fld001, turbJet.fld002, ...and so on. >> type in visnek turbJet in your terminal, and generate *turbJet.nek5000*. >> >> This .nek5000 file can be read by visit. >> >> Thanks, >> Tanmoy >> >> >> On Sat, Dec 7, 2013 at 10:33 AM, > > wrote: >> >> Hi Tanmoy, >> Many thanks. It seems that after dividing by 4 (dt=0.005) it runs >> and I get output files in the form jet0.fxxxxx . >> Now I am trying to visualize them using the precompiled ubuntu11 >> version of visit. Unfortunately, I get the following error: >> >> VisIt could not read from the file >> "/home/galanti/COMPUTATION/__NEK5000/nek5_svn/TEST-__ >> examples/turbJet/jet0.f* >> >> database". >> >> The generated error message was: >> >> There was an error opening >> /home/galanti/COMPUTATION/__NEK5000/nek5_svn/TEST-__ >> examples/turbJet/jet0.f* >> >> database. It may be an invalid file. VisIt tried using the >> following file format readers to open the file: Nek5000 >> >> The following error(s) may be helpful in identifying the problem: >> When attempting to use "Nek", the file matched the general format >> expected by the reader but eventually encountered this error: "A tag >> called filetemplate: must be specified". >> >> What's wrong? >> Many thanks again, >> Barak >> >> >> >> On 12/07/2013 12:42 AM, nek5000-users at lists.mcs.anl.__gov >> >> wrote: >> >> Hi Barak, >> >> It is a problem with numerical Stability. Decrease DT in your >> .rea file >> until the simulations become stable. You could start with 1/2 DT >> to >> check if simulation is stable, other wise go for 1/4 DT, and >> check with >> this simple test. >> >> Thanks, >> Tanmoy >> >> >> On Fri, Dec 6, 2013 at 3:31 PM, >> > >> > >> >> wrote: >> >> Hello, >> I am testing the example turbJet, and it seems that I have >> some >> problem with output. This are the output files: >> jet0.f00001 >> >> Moreover, the ran stops with emergency exit at time 5.64 >> (CFL too >> large?): >> >> >> 282 DNORM, DIVEX 6.2789891850172769E-004 >> 8.4967723454134898E-006 >> 282 5.6400E+00 1.1065E+01 Fluid done >> 282 5.6400000E+00 1.1955953E-03 6.4269380E-04 >> 9.9999991E-01 e2 >> t max/min: 0.0000000000000000 0.0000000000000000 >> CFL, Ctarg! 22.504301079496056 2.0000000000000000 >> call outfld: ifpsco: T >> >> 283 5.6400E+00 Write checkpoint: >> 0 283 OPEN: jet0.f00001 >> >> 283 5.6400E+00 done :: Write checkpoint >> file size = 55. MB >> avg data-throughput = >> 572.1MB/s >> io-nodes = 1 >> >> >> 7 Emergency exit: 283 time = >> 5.6399999999999677 >> Latest solution and data are dumped for post-processing. >> *** STOP *** >> 3 Emergency exit: 283 time = >> 5.6399999999999677 >> Latest solution and data are dumped for post-processing. >> *** STOP *** >> 5 Emergency exit: 283 time = >> 5.6399999999999677 >> Latest solution and data are dumped for post-processing. >> *** STOP *** >> 0 Emergency exit: 283 time = >> 5.6399999999999677 >> Latest solution and data are dumped for post-processing. >> *** STOP *** >> 6 Emergency exit: 283 time = >> 5.6399999999999677 >> Latest solution and data are dumped for post-processing. >> *** STOP *** >> 4 Emergency exit: 283 time = >> 5.6399999999999677 >> Latest solution and data are dumped for post-processing. >> *** STOP *** >> 2 Emergency exit: 283 time = >> 5.6399999999999677 >> Latest solution and data are dumped for post-processing. >> *** STOP *** >> 1 Emergency exit: 283 time = >> 5.6399999999999677 >> >> >> >> >> Thank you, >> Barak >> >> >> ___________________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.____gov >> > > >> https://lists.mcs.anl.gov/____mailman/listinfo/nek5000-users >> >> > __> >> >> >> >> >> >> >> _________________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.__gov >> >> https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users >> >> >> >> _________________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.__gov >> >> https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users >> >> >> >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Dec 9 16:59:44 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 10 Dec 2013 00:59:44 +0200 Subject: [Nek5000-users] turbJet problem In-Reply-To: References: Message-ID: Hi Tanmoy, It is the 4th time that the program stops (probably because of two big dt). See the end of the log of the run. The time step is dt=1e-3. The first test it was 0.02. It seems that the time step has to be reduced when the jet develops considerably. Perhaps, the best thing to do is to simulate till the time limit when the time step becomes not enough small, to stop, and then restart with the next time step (decreased) till the next stage and so on. Now I have further questions: 1. I noticed that there is a parameter to control the error of divergence. If I choose smaller value, how it ncrease the simulation time? 2. I am interested in the Lagrangian properties of the flow, i.e. calculating velocity, vorticity or other velocity derivatives at the Lagrangian orbit. Is it possible and which are the available tools? Barak On 12/09/2013 02:56 AM, nek5000-users at lists.mcs.anl.gov wrote: > Hi Barak, > > I am not aware of variable time stepping in nek5000. The time stepping > used is BDFk/EXTk with CFL constraint for stability. You can change > TORDER in .rea file to 2 or 3 to make the time stepping 2nd or third > order accurate. There is a characteristic based time-stepping though... > IFCHAR in .rea file. > > However, if for a value ot DT you are getting convergence, essentially > you should get the same for smaller value of DT. What is the error you > are getting after the program aborts after 1200 iterations? It is still > stored in your log file I suppose. > > Thanks, > Tanmoy > > > On Sun, Dec 8, 2013 at 12:26 PM, > wrote: > > Hi Tanmoy, > I have divided by 4 and again my run stopped at iteration 1200. My > question is: does nek5000 have variable time-stepping? > Thanks, > Barak > > > On 12/07/2013 08:37 PM, nek5000-users at lists.mcs.anl.__gov > wrote: > > Hi Barak, > > it is because of the fact that the generated file format is > probably not > readable in visit. In the *usrchk* subroutine in your .usr file > write > > these 2 lines > param(66) = 4 > param(67) = 4 > > before the end of the routine > > Then compile and execute your program. Now you will get output > files in > the form of turbJet.fld001, turbJet.fld002, ...and so on. > type in visnek turbJet in your terminal, and generate > *turbJet.nek5000*. > > This .nek5000 file can be read by visit. > > Thanks, > Tanmoy > > > On Sat, Dec 7, 2013 at 10:33 AM, > > >> wrote: > > Hi Tanmoy, > Many thanks. It seems that after dividing by 4 (dt=0.005) > it runs > and I get output files in the form jet0.fxxxxx . > Now I am trying to visualize them using the precompiled > ubuntu11 > version of visit. Unfortunately, I get the following error: > > VisIt could not read from the file > > "/home/galanti/COMPUTATION/____NEK5000/nek5_svn/TEST-____examples/turbJet/jet0.f* > > database". > > The generated error message was: > > There was an error opening > > /home/galanti/COMPUTATION/____NEK5000/nek5_svn/TEST-____examples/turbJet/jet0.f* > > database. It may be an invalid file. VisIt tried using the > following file format readers to open the file: Nek5000 > > The following error(s) may be helpful in identifying the > problem: > When attempting to use "Nek", the file matched the general > format > expected by the reader but eventually encountered this > error: "A tag > called filetemplate: must be specified". > > What's wrong? > Many thanks again, > Barak > > > > On 12/07/2013 12:42 AM, nek5000-users at lists.mcs.anl.____gov > > > wrote: > > Hi Barak, > > It is a problem with numerical Stability. Decrease DT > in your > .rea file > until the simulations become stable. You could start > with 1/2 DT to > check if simulation is stable, other wise go for 1/4 > DT, and > check with > this simple test. > > Thanks, > Tanmoy > > > On Fri, Dec 6, 2013 at 3:31 PM, > > > ____mcs.anl.gov > > >>> wrote: > > Hello, > I am testing the example turbJet, and it seems > that I have some > problem with output. This are the output files: > jet0.f00001 > > Moreover, the ran stops with emergency exit at > time 5.64 > (CFL too > large?): > > > 282 DNORM, DIVEX 6.2789891850172769E-004 > 8.4967723454134898E-006 > 282 5.6400E+00 1.1065E+01 Fluid done > 282 5.6400000E+00 1.1955953E-03 6.4269380E-04 > 9.9999991E-01 e2 > t max/min: 0.0000000000000000 > 0.0000000000000000 > CFL, Ctarg! 22.504301079496056 > 2.0000000000000000 > call outfld: ifpsco: T > > 283 5.6400E+00 Write checkpoint: > 0 283 OPEN: jet0.f00001 > > 283 5.6400E+00 done :: Write checkpoint > file size = > 55. MB > avg data-throughput = > 572.1MB/s > io-nodes = 1 > > > 7 Emergency exit: 283 time = > 5.6399999999999677 > Latest solution and data are dumped for > post-processing. > *** STOP *** > 3 Emergency exit: 283 time = > 5.6399999999999677 > Latest solution and data are dumped for > post-processing. > *** STOP *** > 5 Emergency exit: 283 time = > 5.6399999999999677 > Latest solution and data are dumped for > post-processing. > *** STOP *** > 0 Emergency exit: 283 time = > 5.6399999999999677 > Latest solution and data are dumped for > post-processing. > *** STOP *** > 6 Emergency exit: 283 time = > 5.6399999999999677 > Latest solution and data are dumped for > post-processing. > *** STOP *** > 4 Emergency exit: 283 time = > 5.6399999999999677 > Latest solution and data are dumped for > post-processing. > *** STOP *** > 2 Emergency exit: 283 time = > 5.6399999999999677 > Latest solution and data are dumped for > post-processing. > *** STOP *** > 1 Emergency exit: 283 time = > 5.6399999999999677 > > > > > Thank you, > Barak > > > _____________________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.______gov > ____mcs.anl.gov > >> > https://lists.mcs.anl.gov/______mailman/listinfo/nek5000-users > > > __> > > > > __>__> > > > > > > > ___________________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.____gov > > > https://lists.mcs.anl.gov/____mailman/listinfo/nek5000-users > > > __> > > > ___________________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.____gov > > > https://lists.mcs.anl.gov/____mailman/listinfo/nek5000-users > > __> > > > > > _________________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.__gov > > https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users > > > > _________________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.__gov > > https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users > > > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -------------- next part -------------- A non-text attachment was scrubbed... Name: err-run.log Type: text/x-log Size: 6265 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Mon Dec 9 17:23:45 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 9 Dec 2013 16:23:45 -0700 Subject: [Nek5000-users] turbJet problem In-Reply-To: References: Message-ID: Hi Barak, Your err-run.log clearly shows CFL number increases considerably. So, it is indeed a problem of time-stepping stability. So, as you suggest a variable time-stepping might be necessary. you could even write a small routine in .usr file to control your timestep DT. If you decrease your error of divergence, it has nothing to do with simulation time. You can control simulation time with NSTEPS of .rea file. However for explicit method the region of stability of higher accuracy methods are smaller. So, 3rd order accurate method is a little less stable. You could also try changing TORDER = 2 , when your jet develops considerably. I heard lagrangian formuation could be used in nek5000, but unfortunately I do not know that. It will be nice if you post this question of lagrangian part in an open format, so that the best person in the knowledge of this may answer you. Thanks, Tanmoy On Mon, Dec 9, 2013 at 3:59 PM, wrote: > Hi Tanmoy, > It is the 4th time that the program stops (probably because of two big > dt). See the end of the log of the run. The time step is dt=1e-3. The first > test it was 0.02. It seems that the time step has to be reduced when the > jet develops considerably. > Perhaps, the best thing to do is to simulate till the time limit when the > time step becomes not enough small, to stop, and then restart with the next > time step (decreased) till the next stage and so on. > Now I have further questions: > 1. I noticed that there is a parameter to control the error of divergence. > If I choose smaller value, how it ncrease the simulation time? > 2. I am interested in the Lagrangian properties of the flow, i.e. > calculating velocity, vorticity or other velocity derivatives at the > Lagrangian orbit. Is it possible and which are the available tools? > > Barak > > > > On 12/09/2013 02:56 AM, nek5000-users at lists.mcs.anl.gov wrote: > >> Hi Barak, >> >> I am not aware of variable time stepping in nek5000. The time stepping >> used is BDFk/EXTk with CFL constraint for stability. You can change >> TORDER in .rea file to 2 or 3 to make the time stepping 2nd or third >> order accurate. There is a characteristic based time-stepping though... >> IFCHAR in .rea file. >> >> However, if for a value ot DT you are getting convergence, essentially >> you should get the same for smaller value of DT. What is the error you >> are getting after the program aborts after 1200 iterations? It is still >> stored in your log file I suppose. >> >> Thanks, >> Tanmoy >> >> >> On Sun, Dec 8, 2013 at 12:26 PM, > > wrote: >> >> Hi Tanmoy, >> I have divided by 4 and again my run stopped at iteration 1200. My >> question is: does nek5000 have variable time-stepping? >> Thanks, >> Barak >> >> >> On 12/07/2013 08:37 PM, nek5000-users at lists.mcs.anl.__gov >> >> wrote: >> >> Hi Barak, >> >> it is because of the fact that the generated file format is >> probably not >> readable in visit. In the *usrchk* subroutine in your .usr file >> write >> >> these 2 lines >> param(66) = 4 >> param(67) = 4 >> >> before the end of the routine >> >> Then compile and execute your program. Now you will get output >> files in >> the form of turbJet.fld001, turbJet.fld002, ...and so on. >> type in visnek turbJet in your terminal, and generate >> *turbJet.nek5000*. >> >> This .nek5000 file can be read by visit. >> >> Thanks, >> Tanmoy >> >> >> On Sat, Dec 7, 2013 at 10:33 AM, >> > >> > >> wrote: >> >> Hi Tanmoy, >> Many thanks. It seems that after dividing by 4 (dt=0.005) >> it runs >> and I get output files in the form jet0.fxxxxx . >> Now I am trying to visualize them using the precompiled >> ubuntu11 >> version of visit. Unfortunately, I get the following error: >> >> VisIt could not read from the file >> >> "/home/galanti/COMPUTATION/____NEK5000/nek5_svn/TEST-____ >> examples/turbJet/jet0.f* >> >> >> database". >> >> The generated error message was: >> >> There was an error opening >> >> /home/galanti/COMPUTATION/____NEK5000/nek5_svn/TEST-____ >> examples/turbJet/jet0.f* >> >> >> database. It may be an invalid file. VisIt tried using the >> following file format readers to open the file: Nek5000 >> >> The following error(s) may be helpful in identifying the >> problem: >> When attempting to use "Nek", the file matched the general >> format >> expected by the reader but eventually encountered this >> error: "A tag >> called filetemplate: must be specified". >> >> What's wrong? >> Many thanks again, >> Barak >> >> >> >> On 12/07/2013 12:42 AM, nek5000-users at lists.mcs.anl.____gov >> >> >> > > wrote: >> >> Hi Barak, >> >> It is a problem with numerical Stability. Decrease DT >> in your >> .rea file >> until the simulations become stable. You could start >> with 1/2 DT to >> check if simulation is stable, other wise go for 1/4 >> DT, and >> check with >> this simple test. >> >> Thanks, >> Tanmoy >> >> >> On Fri, Dec 6, 2013 at 3:31 PM, >> > > > >> > ____mcs.anl.gov >> >> >> > >>> wrote: >> >> Hello, >> I am testing the example turbJet, and it seems >> that I have some >> problem with output. This are the output files: >> jet0.f00001 >> >> Moreover, the ran stops with emergency exit at >> time 5.64 >> (CFL too >> large?): >> >> >> 282 DNORM, DIVEX 6.2789891850172769E-004 >> 8.4967723454134898E-006 >> 282 5.6400E+00 1.1065E+01 Fluid done >> 282 5.6400000E+00 1.1955953E-03 6.4269380E-04 >> 9.9999991E-01 e2 >> t max/min: 0.0000000000000000 >> 0.0000000000000000 >> CFL, Ctarg! 22.504301079496056 >> 2.0000000000000000 >> call outfld: ifpsco: T >> >> 283 5.6400E+00 Write checkpoint: >> 0 283 OPEN: jet0.f00001 >> >> 283 5.6400E+00 done :: Write checkpoint >> file size = >> 55. MB >> avg data-throughput = >> 572.1MB/s >> io-nodes = 1 >> >> >> 7 Emergency exit: 283 time = >> 5.6399999999999677 >> Latest solution and data are dumped for >> post-processing. >> *** STOP *** >> 3 Emergency exit: 283 time = >> 5.6399999999999677 >> Latest solution and data are dumped for >> post-processing. >> *** STOP *** >> 5 Emergency exit: 283 time = >> 5.6399999999999677 >> Latest solution and data are dumped for >> post-processing. >> *** STOP *** >> 0 Emergency exit: 283 time = >> 5.6399999999999677 >> Latest solution and data are dumped for >> post-processing. >> *** STOP *** >> 6 Emergency exit: 283 time = >> 5.6399999999999677 >> Latest solution and data are dumped for >> post-processing. >> *** STOP *** >> 4 Emergency exit: 283 time = >> 5.6399999999999677 >> Latest solution and data are dumped for >> post-processing. >> *** STOP *** >> 2 Emergency exit: 283 time = >> 5.6399999999999677 >> Latest solution and data are dumped for >> post-processing. >> *** STOP *** >> 1 Emergency exit: 283 time = >> 5.6399999999999677 >> >> >> >> >> Thank you, >> Barak >> >> >> ______________________________ >> _______________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.______gov >> > ____mcs.anl.gov >> > >> >> https://lists.mcs.anl.gov/______mailman/listinfo/nek5000-users >> >> >> > __> >> >> >> > >> >> > __>__> >> >> >> >> >> >> >> ___________________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.____gov >> > > >> https://lists.mcs.anl.gov/____mailman/listinfo/nek5000-users >> >> >> > __> >> >> >> ___________________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.____gov >> > > >> https://lists.mcs.anl.gov/____mailman/listinfo/nek5000-users >> >> > __> >> >> >> >> >> _________________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.__gov >> >> https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users >> >> >> >> _________________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.__gov >> >> https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users >> >> >> >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Dec 9 17:32:07 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 10 Dec 2013 01:32:07 +0200 Subject: [Nek5000-users] turbJet problem In-Reply-To: References: Message-ID: Hi Tanmoy, Thank you for the nice reply. Hmm, considering restart: is it possible? this could also be an alternative considering the issue of decreasing time step. Now how could I post my question in open format? Thanks again Barak On 12/10/2013 01:23 AM, nek5000-users at lists.mcs.anl.gov wrote: > Hi Barak, > > Your err-run.log clearly shows CFL number increases considerably. So, it > is indeed a problem of time-stepping stability. So, as you suggest a > variable time-stepping might be necessary. you could even write a small > routine in .usr file to control your timestep DT. If you decrease your > error of divergence, it has nothing to do with simulation time. You can > control simulation time with NSTEPS of .rea file. However for explicit > method the region of stability of higher accuracy methods are smaller. > So, 3rd order accurate method is a little less stable. You could also > try changing TORDER = 2 , when your jet develops considerably. > > I heard lagrangian formuation could be used in nek5000, but > unfortunately I do not know that. It will be nice if you post this > question of lagrangian part in an open format, so that the best person > in the knowledge of this may answer you. > > Thanks, > > Tanmoy > > > On Mon, Dec 9, 2013 at 3:59 PM, > wrote: > > Hi Tanmoy, > It is the 4th time that the program stops (probably because of two > big dt). See the end of the log of the run. The time step is > dt=1e-3. The first test it was 0.02. It seems that the time step has > to be reduced when the jet develops considerably. > Perhaps, the best thing to do is to simulate till the time limit > when the time step becomes not enough small, to stop, and then > restart with the next time step (decreased) till the next stage and > so on. > Now I have further questions: > 1. I noticed that there is a parameter to control the error of > divergence. If I choose smaller value, how it ncrease the simulation > time? > 2. I am interested in the Lagrangian properties of the flow, i.e. > calculating velocity, vorticity or other velocity derivatives at the > Lagrangian orbit. Is it possible and which are the available tools? > > Barak > > > > On 12/09/2013 02:56 AM, nek5000-users at lists.mcs.anl.__gov > wrote: > > Hi Barak, > > I am not aware of variable time stepping in nek5000. The time > stepping > used is BDFk/EXTk with CFL constraint for stability. You can change > TORDER in .rea file to 2 or 3 to make the time stepping 2nd or third > order accurate. There is a characteristic based time-stepping > though... > IFCHAR in .rea file. > > However, if for a value ot DT you are getting convergence, > essentially > you should get the same for smaller value of DT. What is the > error you > are getting after the program aborts after 1200 iterations? It > is still > stored in your log file I suppose. > > Thanks, > Tanmoy > > > On Sun, Dec 8, 2013 at 12:26 PM, > > >> wrote: > > Hi Tanmoy, > I have divided by 4 and again my run stopped at iteration > 1200. My > question is: does nek5000 have variable time-stepping? > Thanks, > Barak > > > On 12/07/2013 08:37 PM, nek5000-users at lists.mcs.anl.____gov > > > wrote: > > Hi Barak, > > it is because of the fact that the generated file format is > probably not > readable in visit. In the *usrchk* subroutine in your > .usr file > write > > these 2 lines > param(66) = 4 > param(67) = 4 > > before the end of the routine > > Then compile and execute your program. Now you will get > output > files in > the form of turbJet.fld001, turbJet.fld002, ...and so on. > type in visnek turbJet in your terminal, and generate > *turbJet.nek5000*. > > This .nek5000 file can be read by visit. > > Thanks, > Tanmoy > > > On Sat, Dec 7, 2013 at 10:33 AM, > > > ____mcs.anl.gov > >>> wrote: > > Hi Tanmoy, > Many thanks. It seems that after dividing by 4 > (dt=0.005) > it runs > and I get output files in the form jet0.fxxxxx . > Now I am trying to visualize them using the > precompiled > ubuntu11 > version of visit. Unfortunately, I get the > following error: > > VisIt could not read from the file > > > "/home/galanti/COMPUTATION/______NEK5000/nek5_svn/TEST-______examples/turbJet/jet0.f* > > > database". > > The generated error message was: > > There was an error opening > > > /home/galanti/COMPUTATION/______NEK5000/nek5_svn/TEST-______examples/turbJet/jet0.f* > > > database. It may be an invalid file. VisIt tried > using the > following file format readers to open the file: > Nek5000 > > The following error(s) may be helpful in > identifying the > problem: > When attempting to use "Nek", the file matched the > general > format > expected by the reader but eventually encountered this > error: "A tag > called filetemplate: must be specified". > > What's wrong? > Many thanks again, > Barak > > > > On 12/07/2013 12:42 AM, > nek5000-users at lists.mcs.anl.______gov > > > ____mcs.anl.gov > >> wrote: > > Hi Barak, > > It is a problem with numerical Stability. > Decrease DT > in your > .rea file > until the simulations become stable. You could > start > with 1/2 DT to > check if simulation is stable, other wise go > for 1/4 > DT, and > check with > this simple test. > > Thanks, > Tanmoy > > > On Fri, Dec 6, 2013 at 3:31 PM, > ____mcs.anl.gov > >> > . > .>______mcs.anl.gov > > > > ____mcs.anl.gov > >>>> wrote: > > Hello, > I am testing the example turbJet, and it > seems > that I have some > problem with output. This are the output > files: > jet0.f00001 > > Moreover, the ran stops with emergency > exit at > time 5.64 > (CFL too > large?): > > > 282 DNORM, DIVEX > 6.2789891850172769E-004 > 8.4967723454134898E-006 > 282 5.6400E+00 1.1065E+01 > Fluid done > 282 5.6400000E+00 1.1955953E-03 > 6.4269380E-04 > 9.9999991E-01 e2 > t max/min: 0.0000000000000000 > 0.0000000000000000 > CFL, Ctarg! 22.504301079496056 > 2.0000000000000000 > call outfld: ifpsco: T > > 283 5.6400E+00 Write checkpoint: > 0 283 OPEN: jet0.f00001 > > 283 5.6400E+00 done :: Write > checkpoint > file size = > 55. MB > avg > data-throughput = > 572.1MB/s > io-nodes = > 1 > > > 7 Emergency exit: > 283 time = > 5.6399999999999677 > Latest solution and data are dumped for > post-processing. > *** STOP *** > 3 Emergency exit: > 283 time = > 5.6399999999999677 > Latest solution and data are dumped for > post-processing. > *** STOP *** > 5 Emergency exit: > 283 time = > 5.6399999999999677 > Latest solution and data are dumped for > post-processing. > *** STOP *** > 0 Emergency exit: > 283 time = > 5.6399999999999677 > Latest solution and data are dumped for > post-processing. > *** STOP *** > 6 Emergency exit: > 283 time = > 5.6399999999999677 > Latest solution and data are dumped for > post-processing. > *** STOP *** > 4 Emergency exit: > 283 time = > 5.6399999999999677 > Latest solution and data are dumped for > post-processing. > *** STOP *** > 2 Emergency exit: > 283 time = > 5.6399999999999677 > Latest solution and data are dumped for > post-processing. > *** STOP *** > 1 Emergency exit: > 283 time = > 5.6399999999999677 > > > > > Thank you, > Barak > > > > _______________________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.________gov > . > .>______mcs.anl.gov > > ____mcs.anl.gov > >>> > https://lists.mcs.anl.gov/________mailman/listinfo/nek5000-__users > > > > > > > > > __>__> > > > > > > __> > > > > > __>__>__> > > > > > > > > _____________________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.______gov > ____mcs.anl.gov > >> > https://lists.mcs.anl.gov/______mailman/listinfo/nek5000-users > > > __> > > > > > __>__> > > > _____________________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.______gov > ____mcs.anl.gov > >> > https://lists.mcs.anl.gov/______mailman/listinfo/nek5000-users > > > __> > > > > __>__> > > > > > ___________________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.____gov > > > https://lists.mcs.anl.gov/____mailman/listinfo/nek5000-users > > > __> > > > ___________________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.____gov > > > https://lists.mcs.anl.gov/____mailman/listinfo/nek5000-users > > __> > > > > > _________________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.__gov > > https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users > > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Tue Dec 10 06:00:12 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 10 Dec 2013 14:00:12 +0200 Subject: [Nek5000-users] Lagrangian particle tracking In-Reply-To: References: Message-ID: Hi I am interested to know if there is an example for the Lagrangian particle tracking as described in http://nek5000.mcs.anl.gov/index.php/Data_processing_example . Thanks, Barak Galanti -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Dec 10 07:27:17 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 10 Dec 2013 14:27:17 +0100 Subject: [Nek5000-users] Lagrangian particle tracking In-Reply-To: References: Message-ID: Le 10/12/2013 13:00, nek5000-users at lists.mcs.anl.gov a ?crit Hello, What do you want to known about Lagrangian Particle Tracking ? Anne Tani?re > > Hi > I am interested to know if there is an example for the Lagrangian > particle tracking > as described in > http://nek5000.mcs.anl.gov/index.php/Data_processing_example . > > Thanks, > Barak Galanti > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -- Pr. Anne Tani?re, Lorraine University Nouvel email: anne.taniere at univ-lorraine.fr Responsable des stages 5A, MFE ESSTIN tel : 03.83.68.50.83 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Dec 10 16:25:19 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 11 Dec 2013 00:25:19 +0200 Subject: [Nek5000-users] Lagrangian particle tracking In-Reply-To: References: Message-ID: On 12/10/2013 03:27 PM, nek5000-users at lists.mcs.anl.gov wrote: > Le 10/12/2013 13:00, nek5000-users at lists.mcs.anl.gov a ?crit > > Hello, > > What do you want to known about Lagrangian Particle Tracking ? Hi Anne, I would like to perform some Lagrangian particle simulation to to compute the component of the velocity field or vorticity at the particle. Do you have example for such computation as described in the webpage: http://nek5000.mcs.anl.gov/index.php/Data_processing_example Thanks, Barak > > Anne Tani?re >> >> Hi >> I am interested to know if there is an example for the Lagrangian >> particle tracking >> as described in >> http://nek5000.mcs.anl.gov/index.php/Data_processing_example . >> >> Thanks, >> Barak Galanti >> >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > -- > Pr. Anne Tani?re, Lorraine University > Nouvel email:anne.taniere at univ-lorraine.fr > Responsable des stages 5A, MFE ESSTIN > tel : 03.83.68.50.83 > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Tue Dec 10 18:51:56 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 10 Dec 2013 18:51:56 -0600 (CST) Subject: [Nek5000-users] Lagrangian particle tracking In-Reply-To: Message-ID: Hi, I've added a Lagrangian particle tracking example --- examples/hemi look at hemi.usr. It produces a sequence of files with particle positions and a matlab script is provided for viewing. As soon as I have a chance I'll also develop a script for visit. Paul ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Tuesday, December 10, 2013 4:25:19 PM Subject: Re: [Nek5000-users] Lagrangian particle tracking On 12/10/2013 03:27 PM, nek5000-users at lists.mcs.anl.gov wrote: > Le 10/12/2013 13:00, nek5000-users at lists.mcs.anl.gov a ?crit > > Hello, > > What do you want to known about Lagrangian Particle Tracking ? Hi Anne, I would like to perform some Lagrangian particle simulation to to compute the component of the velocity field or vorticity at the particle. Do you have example for such computation as described in the webpage: http://nek5000.mcs.anl.gov/index.php/Data_processing_example Thanks, Barak > > Anne Tani?re >> >> Hi >> I am interested to know if there is an example for the Lagrangian >> particle tracking >> as described in >> http://nek5000.mcs.anl.gov/index.php/Data_processing_example . >> >> Thanks, >> Barak Galanti >> >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > -- > Pr. Anne Tani?re, Lorraine University > Nouvel email:anne.taniere at univ-lorraine.fr > Responsable des stages 5A, MFE ESSTIN > tel : 03.83.68.50.83 > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Wed Dec 11 02:07:00 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 11 Dec 2013 10:07:00 +0200 Subject: [Nek5000-users] Lagrangian particle tracking In-Reply-To: References: Message-ID: Hi Paul, Many thanks for the example. I will have a look on the code later on today and let you know if I have further questions. Another questions: 1. Does nek also deal with moving objects/boundaries? Do you have an example for a free fall solid body? 2. How does a decrease in the parameter of the divergence error increase the computation time? Many thanks, Barak On 12/11/2013 02:51 AM, nek5000-users at lists.mcs.anl.gov wrote: > > Hi, > > I've added a Lagrangian particle tracking example --- > > examples/hemi > > look at hemi.usr. > > It produces a sequence of files with particle positions and > a matlab script is provided for viewing. As soon as I have > a chance I'll also develop a script for visit. > > Paul > > > ----- Original Message ----- > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Sent: Tuesday, December 10, 2013 4:25:19 PM > Subject: Re: [Nek5000-users] Lagrangian particle tracking > > On 12/10/2013 03:27 PM, nek5000-users at lists.mcs.anl.gov wrote: >> Le 10/12/2013 13:00, nek5000-users at lists.mcs.anl.gov a ?crit > >> >> Hello, >> >> What do you want to known about Lagrangian Particle Tracking ? > > > Hi Anne, > I would like to perform some Lagrangian particle simulation to to > compute the component of the velocity field or vorticity at the > particle. Do you have example for such computation as described in the > webpage: > http://nek5000.mcs.anl.gov/index.php/Data_processing_example > Thanks, > > Barak > >> >> Anne Tani?re >>> >>> Hi >>> I am interested to know if there is an example for the Lagrangian >>> particle tracking >>> as described in >>> http://nek5000.mcs.anl.gov/index.php/Data_processing_example . >>> >>> Thanks, >>> Barak Galanti >>> >>> >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> >> -- >> Pr. Anne Tani?re, Lorraine University >> Nouvel email:anne.taniere at univ-lorraine.fr >> Responsable des stages 5A, MFE ESSTIN >> tel : 03.83.68.50.83 >> >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Thu Dec 12 08:47:29 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 12 Dec 2013 15:47:29 +0100 Subject: [Nek5000-users] Magnetic boundary conditions (especially (quasi) vacuum conditions) Message-ID: Hello everyone, I just started using Nek5000 and my group is currently thinking about using the code to simulate a precession driven dynamo in a ellipsoidal shell. For this, we would need to run an MHD Simulation with vacuum or quasi vacuum boundary conditions (the code we used so far used quasi vacuum conditions). Has anyone experience with implementing either of those? I found an older post (http://lists.mcs.anl.gov/pipermail/nek5000-users/2011-July/001416.html) that mentioned bc's for the magnetic field that are different from the velocity conditions, but could not find any update on this. Best whishes, Jan From nek5000-users at lists.mcs.anl.gov Thu Dec 12 08:54:59 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 12 Dec 2013 15:54:59 +0100 Subject: [Nek5000-users] nek5000 manual Message-ID: Dear neks, where can i find the the latest version of the NEK5000 manual? Thanks a lot, Matteo -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Dec 12 09:02:07 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 12 Dec 2013 09:02:07 -0600 Subject: [Nek5000-users] nek5000 manual In-Reply-To: References: Message-ID: Hi Matteo, You can find the latest version of the manual as well as some getting started info at: http://nek5000.mcs.anl.gov/index.php/UG The most recent version in the 2010 manual. Best, Katherine On Thu, Dec 12, 2013 at 8:54 AM, wrote: > Dear neks, > where can i find the the latest version of the NEK5000 manual? > > Thanks a lot, > Matteo > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Dec 12 12:06:44 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 12 Dec 2013 20:06:44 +0200 Subject: [Nek5000-users] Lagrangian particle tracking In-Reply-To: References: Message-ID: Hei Paul, I tried your example and I get just at the beginning an error. See the attached file. Thanks, Barak On 12/11/2013 02:51 AM, nek5000-users at lists.mcs.anl.gov wrote: > > Hi, > > I've added a Lagrangian particle tracking example --- > > examples/hemi > > look at hemi.usr. > > It produces a sequence of files with particle positions and > a matlab script is provided for viewing. As soon as I have > a chance I'll also develop a script for visit. > > Paul > > > ----- Original Message ----- > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Sent: Tuesday, December 10, 2013 4:25:19 PM > Subject: Re: [Nek5000-users] Lagrangian particle tracking > > On 12/10/2013 03:27 PM, nek5000-users at lists.mcs.anl.gov wrote: >> Le 10/12/2013 13:00, nek5000-users at lists.mcs.anl.gov a ?crit > >> >> Hello, >> >> What do you want to known about Lagrangian Particle Tracking ? > > > Hi Anne, > I would like to perform some Lagrangian particle simulation to to > compute the component of the velocity field or vorticity at the > particle. Do you have example for such computation as described in the > webpage: > http://nek5000.mcs.anl.gov/index.php/Data_processing_example > Thanks, > > Barak > >> >> Anne Tani?re >>> >>> Hi >>> I am interested to know if there is an example for the Lagrangian >>> particle tracking >>> as described in >>> http://nek5000.mcs.anl.gov/index.php/Data_processing_example . >>> >>> Thanks, >>> Barak Galanti >>> >>> >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> >> -- >> Pr. Anne Tani?re, Lorraine University >> Nouvel email:anne.taniere at univ-lorraine.fr >> Responsable des stages 5A, MFE ESSTIN >> tel : 03.83.68.50.83 >> >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -------------- next part -------------- A non-text attachment was scrubbed... Name: hemi-run.log Type: text/x-log Size: 17099 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Thu Dec 12 14:14:43 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 12 Dec 2013 14:14:43 -0600 Subject: [Nek5000-users] Lagrangian particle tracking In-Reply-To: References: Message-ID: Hi Barak, I believe your error is a result of a compiler specific update. I have updated the Nek source code to hopefully address this issue. Please update your code and let me know if the problem is not resolved. Thanks Katherine On Thu, Dec 12, 2013 at 12:06 PM, wrote: > Hei Paul, > I tried your example and I get just at the beginning an error. See the > attached file. > > Thanks, > Barak > > On 12/11/2013 02:51 AM, nek5000-users at lists.mcs.anl.gov wrote: > >> >> Hi, >> >> I've added a Lagrangian particle tracking example --- >> >> examples/hemi >> >> look at hemi.usr. >> >> It produces a sequence of files with particle positions and >> a matlab script is provided for viewing. As soon as I have >> a chance I'll also develop a script for visit. >> >> Paul >> >> >> ----- Original Message ----- >> From: nek5000-users at lists.mcs.anl.gov >> To: nek5000-users at lists.mcs.anl.gov >> Sent: Tuesday, December 10, 2013 4:25:19 PM >> Subject: Re: [Nek5000-users] Lagrangian particle tracking >> >> On 12/10/2013 03:27 PM, nek5000-users at lists.mcs.anl.gov wrote: >> >>> Le 10/12/2013 13:00, nek5000-users at lists.mcs.anl.gov a ?crit >>> >> >> >>> Hello, >>> >>> What do you want to known about Lagrangian Particle Tracking ? >>> >> >> >> Hi Anne, >> I would like to perform some Lagrangian particle simulation to to >> compute the component of the velocity field or vorticity at the >> particle. Do you have example for such computation as described in the >> webpage: >> http://nek5000.mcs.anl.gov/index.php/Data_processing_example >> Thanks, >> >> Barak >> >> >>> Anne Tani?re >>> >>>> >>>> Hi >>>> I am interested to know if there is an example for the Lagrangian >>>> particle tracking >>>> as described in >>>> http://nek5000.mcs.anl.gov/index.php/Data_processing_example . >>>> >>>> Thanks, >>>> Barak Galanti >>>> >>>> >>>> >>>> _______________________________________________ >>>> Nek5000-users mailing list >>>> Nek5000-users at lists.mcs.anl.gov >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>> >>> >>> >>> -- >>> Pr. Anne Tani?re, Lorraine University >>> Nouvel email:anne.taniere at univ-lorraine.fr >>> Responsable des stages 5A, MFE ESSTIN >>> tel : 03.83.68.50.83 >>> >>> >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >>> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Dec 12 17:44:07 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 12 Dec 2013 17:44:07 -0600 (CST) Subject: [Nek5000-users] Magnetic boundary conditions (especially (quasi) vacuum conditions) In-Reply-To: Message-ID: Hi Jan, Sounds exciting! As a first step, we have implemented the quasi vacuum boundary/idealized insulator conditions for the boundary aligned with the Cartesian axes -- e.g., use the cbc/genbox character 'ddn' in .rea for Dirichlet conditions on the first two components, Bx & By (with vx=0 & vy=0 for ifield.eq.ifldmhd in userbc) and for homogeneous Neumann on the third, i.e. for dBz/dz=0. I have started debugging its extension for the general case. I am currently tied up with the end of the year projects but I am hopeful that I'll get back to it over the Christmas break. Let me know if you have any questions. Thanks. Aleks ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Thursday, December 12, 2013 8:47:29 AM Subject: [Nek5000-users] Magnetic boundary conditions (especially (quasi) vacuum conditions) Hello everyone, I just started using Nek5000 and my group is currently thinking about using the code to simulate a precession driven dynamo in a ellipsoidal shell. For this, we would need to run an MHD Simulation with vacuum or quasi vacuum boundary conditions (the code we used so far used quasi vacuum conditions). Has anyone experience with implementing either of those? I found an older post (http://lists.mcs.anl.gov/pipermail/nek5000-users/2011-July/001416.html) that mentioned bc's for the magnetic field that are different from the velocity conditions, but could not find any update on this. Best whishes, Jan _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Fri Dec 13 03:44:49 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 13 Dec 2013 11:44:49 +0200 Subject: [Nek5000-users] Lagrangian particle tracking In-Reply-To: References: Message-ID: Hi Katherine, I reinstalled the new version (981) and indeed the code is running. I am going to check now the results. In previous messages I asked: 1. Is the used interpolation spectral? 2. When I decrease the desired divergence error, how does it increase the computation time? 3. Are there examples for moving solid bodies or boundaries? Many thanks. Barak On 12/12/2013 10:14 PM, nek5000-users at lists.mcs.anl.gov wrote: > Hi Barak, > > I believe your error is a result of a compiler specific update. I have > updated the Nek source code to hopefully address this issue. Please > update your code and let me know if the problem is not resolved. > > Thanks > Katherine > > > On Thu, Dec 12, 2013 at 12:06 PM, > wrote: > > Hei Paul, > I tried your example and I get just at the beginning an error. See > the attached file. > > Thanks, > Barak > > On 12/11/2013 02:51 AM, nek5000-users at lists.mcs.anl.__gov > wrote: > > > Hi, > > I've added a Lagrangian particle tracking example --- > > examples/hemi > > look at hemi.usr. > > It produces a sequence of files with particle positions and > a matlab script is provided for viewing. As soon as I have > a chance I'll also develop a script for visit. > > Paul > > > ----- Original Message ----- > From: nek5000-users at lists.mcs.anl.__gov > > To: nek5000-users at lists.mcs.anl.__gov > > Sent: Tuesday, December 10, 2013 4:25:19 PM > Subject: Re: [Nek5000-users] Lagrangian particle tracking > > On 12/10/2013 03:27 PM, nek5000-users at lists.mcs.anl.__gov > wrote: > > Le 10/12/2013 13:00, nek5000-users at lists.mcs.anl.__gov > a ?crit > > > > Hello, > > What do you want to known about Lagrangian Particle > Tracking ? > > > > Hi Anne, > I would like to perform some Lagrangian particle simulation to to > compute the component of the velocity field or vorticity at the > particle. Do you have example for such computation as described > in the > webpage: > http://nek5000.mcs.anl.gov/__index.php/Data_processing___example > > Thanks, > > Barak > > > Anne Tani?re > > > Hi > I am interested to know if there is an example for the > Lagrangian > particle tracking > as described in > http://nek5000.mcs.anl.gov/__index.php/Data_processing___example > > . > > Thanks, > Barak Galanti > > > > _________________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.__gov > > https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users > > > > > -- > Pr. Anne Tani?re, Lorraine University > Nouvel email:anne.taniere at univ-__lorraine.fr > > Responsable des stages 5A, MFE ESSTIN > tel : 03.83.68.50.83 > > > > _________________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.__gov > > https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users > > > > _________________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.__gov > > https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users > > _________________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.__gov > > https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users > > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Fri Dec 13 04:53:46 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 13 Dec 2013 10:53:46 +0000 Subject: [Nek5000-users] fld output Message-ID: Hi Paul, Katie and all, Sorry for the very late reply but I had to interrupt what I was working on. Going back to the problem, I basically would like to understand better how to extract the simulation results from xm1, ym1, zm1, vx, etc. I have been trying to do so in userchk() in the .usr file through postprocessing.. I have been able to extract all the data and print into a custom file format but I am having difficulties in understanding how the data is sorted in xm1, ym1, etc. For instance, I have noticed that the y1/z1 values are sorted in chunks depending on the spectral order/square of the spectral order respectively but are sorted in some strange way.. My aim is to output the data into a custom file format, with for example, all the zm1 values in order, and then subsequently all the ym1 values in order.. without having to go through a sorting algorithm.. i.e. to output directly through some loops by knowing the sorting of the arrays xm1, ym1 etc (Note that I output to f0000* files (binary) and will use MPI I/O too..) Thank you, JP -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Dec 13 07:19:48 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 13 Dec 2013 07:19:48 -0600 (CST) Subject: [Nek5000-users] fld output In-Reply-To: References: Message-ID: Hi JP, The answer to your questions depends on the mesh and the number of processors. Let's assume that you have the simplest possible mesh, i.e., one generated with genbox. Let's further assume you have only one processor. Then the following loops are equivalent: n=nx1*ny1*nz1*nelt do i=1,n write(6,*) xm1(i,1,1,1) enddo integer e do e=1,nelt do k=1,nz1 do j=1,ny1 do i=1,nx1 write(6,*) xm1(i,j,k,e) enddo enddo enddo enddo In other words, the two loops write out the data as it is stored in memory --- with unit stride. (Loop 1 is preferred, because it has better potential for compiler optimization.) In the two processor case, the loops are also equivalent. However, here, the "e" variable points to the local element number, and one does not know until runtime which elements are assigned to which processor----so the mapping of "e" in your mesh (which we typically refer to as eg, for global element number) is an unknown. The array lglel(e) returns eg for each e=1,...,nelt. Regarding the spatial order, if the mesh was generated with genbox, then the elements are lexicographically ordered. Specifically, if you have (in the one processor case): nelt = nelx x nely x nelz, then you would have eg ex ey ez 1 1 1 1 2 2 1 1 3 3 1 1 4 4 1 1 : : 1 1 nelx nelx 1 1 nelx+1 1 2 1 : : : : nelt nelx nely nelz In the multiprocessor case, your custom file format will require communication. Paul On Fri, 13 Dec 2013, nek5000-users at lists.mcs.anl.gov wrote: > Hi Paul, Katie and all, > > Sorry for the very late reply but I had to interrupt what I was working on. > > Going back to the problem, I basically would like to understand better how > to extract the simulation results from xm1, ym1, zm1, vx, etc. > > I have been trying to do so in userchk() in the .usr file through > postprocessing.. I have been able to extract all the data and print into a > custom file format but I am having difficulties in understanding how the > data is sorted in xm1, ym1, etc. For instance, I have noticed that the > y1/z1 values are sorted in chunks depending on the spectral order/square of > the spectral order respectively but are sorted in some strange way.. > > My aim is to output the data into a custom file format, with for example, > all the zm1 values in order, and then subsequently all the ym1 values in > order.. without having to go through a sorting algorithm.. i.e. to output > directly through some loops by knowing the sorting of the arrays xm1, ym1 > etc > > (Note that I output to f0000* files (binary) and will use MPI I/O too..) > > Thank you, > JP > From nek5000-users at lists.mcs.anl.gov Fri Dec 13 09:24:50 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 13 Dec 2013 09:24:50 -0600 (CST) Subject: [Nek5000-users] Lagrangian particle tracking In-Reply-To: Message-ID: Hi Barak, I have just a bit of time but will try to give you some quick answers to start. Interpolation is spectral. Decreasing div error simply sets the iteration tolerance tighter --- meaning that the _discrete_ system is solved to a tighter tolerance (i.e., closer to machine precision). However, it does not mean that the divergence is necessarily smaller, since there is also a discretization error associated with the fact that you are solving the discretized problem and not the continuous one. Discretization error can be reduced by increasing lx1 or the number of elements. If your problem is nondimensionalized in terms of convective timescales, I find div=1.e-6 is generally adequate (except, say, for certain stability problems, which tend to be very sensitive). If you are working in physical units, I would suggest set div=0 and tolrel = 0.01 ---- this will automatically choose tolerances for you. (It tends to be a bit more conservative than the 1.e-6 value that I suggest above.) There is a moving boundary example in the peristaltic flow example (/peris) At present, I don't have any falling body examples. Such a case is either easy or very hard, depending on the flow domain. hth, Paul ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Friday, December 13, 2013 3:44:49 AM Subject: Re: [Nek5000-users] Lagrangian particle tracking Hi Katherine, I reinstalled the new version (981) and indeed the code is running. I am going to check now the results. In previous messages I asked: 1. Is the used interpolation spectral? 2. When I decrease the desired divergence error, how does it increase the computation time? 3. Are there examples for moving solid bodies or boundaries? Many thanks. Barak On 12/12/2013 10:14 PM, nek5000-users at lists.mcs.anl.gov wrote: > Hi Barak, > > I believe your error is a result of a compiler specific update. I have > updated the Nek source code to hopefully address this issue. Please > update your code and let me know if the problem is not resolved. > > Thanks > Katherine > > > On Thu, Dec 12, 2013 at 12:06 PM, > wrote: > > Hei Paul, > I tried your example and I get just at the beginning an error. See > the attached file. > > Thanks, > Barak > > On 12/11/2013 02:51 AM, nek5000-users at lists.mcs.anl.__gov > wrote: > > > Hi, > > I've added a Lagrangian particle tracking example --- > > examples/hemi > > look at hemi.usr. > > It produces a sequence of files with particle positions and > a matlab script is provided for viewing. As soon as I have > a chance I'll also develop a script for visit. > > Paul > > > ----- Original Message ----- > From: nek5000-users at lists.mcs.anl.__gov > > To: nek5000-users at lists.mcs.anl.__gov > > Sent: Tuesday, December 10, 2013 4:25:19 PM > Subject: Re: [Nek5000-users] Lagrangian particle tracking > > On 12/10/2013 03:27 PM, nek5000-users at lists.mcs.anl.__gov > wrote: > > Le 10/12/2013 13:00, nek5000-users at lists.mcs.anl.__gov > a ?crit > > > > Hello, > > What do you want to known about Lagrangian Particle > Tracking ? > > > > Hi Anne, > I would like to perform some Lagrangian particle simulation to to > compute the component of the velocity field or vorticity at the > particle. Do you have example for such computation as described > in the > webpage: > http://nek5000.mcs.anl.gov/__index.php/Data_processing___example > > Thanks, > > Barak > > > Anne Tani?re > > > Hi > I am interested to know if there is an example for the > Lagrangian > particle tracking > as described in > http://nek5000.mcs.anl.gov/__index.php/Data_processing___example > > . > > Thanks, > Barak Galanti > > > > _________________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.__gov > > https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users > > > > > -- > Pr. Anne Tani?re, Lorraine University > Nouvel email:anne.taniere at univ-__lorraine.fr > > Responsable des stages 5A, MFE ESSTIN > tel : 03.83.68.50.83 > > > > _________________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.__gov > > https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users > > > > _________________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.__gov > > https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users > > _________________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.__gov > > https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users > > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Fri Dec 13 11:09:04 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 13 Dec 2013 19:09:04 +0200 Subject: [Nek5000-users] Lagrangian particle tracking In-Reply-To: References: Message-ID: Hi Paul, It helped a lot. But let me insist on the question of accuracy. If the problem is well resolved (and spectrally accurate) then the divergence error could matter. No? I am interested to simulate turbulent flows so, this is the reason why I am concerning about this issue. Thanks again and have a nice weekend. Barak Quoting nek5000-users at lists.mcs.anl.gov: > Hi Barak, > > I have just a bit of time but will try to give you some quick > answers to start. > > Interpolation is spectral. > > Decreasing div error simply sets the iteration tolerance tighter --- > meaning that the _discrete_ system is solved to a tighter tolerance > (i.e., closer to machine precision).? ?However, it does not mean that > the divergence is necessarily smaller, since there is also a discretization > error associated with the fact that you are solving the discretized problem > and not the continuous one.? ?Discretization error can be reduced by > increasing lx1 or the number of elements. > > If your problem is nondimensionalized in terms of convective timescales, > I find div=1.e-6 is generally adequate (except, say, for certain > stability problems, which tend to be very sensitive).? If you are working > in physical units, I would suggest set div=0 and tolrel = 0.01 ---- this > will automatically choose tolerances for you.? (It tends to be a bit more > conservative than the 1.e-6 value that I suggest above.) > > There is a moving boundary example in the peristaltic flow example (/peris) > At present, I don't have any falling body examples.? Such a case is either > easy or very hard, depending on the flow domain. > > hth, > > Paul > > > ----- Original Message ----- > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Sent: Friday, December 13, 2013 3:44:49 AM > Subject: Re: [Nek5000-users] Lagrangian particle tracking > > Hi Katherine, > > I reinstalled the new version (981) and indeed the code is running. I am > going to check now the results. > > In previous messages I asked: > 1. Is the used interpolation spectral? > 2. When I decrease the desired divergence error, how does it increase > the computation time? > 3. Are there examples for moving solid bodies or boundaries? > > Many thanks. > Barak > > On 12/12/2013 10:14 PM, nek5000-users at lists.mcs.anl.gov wrote: > Hi Barak, >> >> I believe your error is a result of a compiler specific update.? I have >> updated the Nek source code to hopefully address this issue.? Please >> update your code and let me know if the problem is not resolved. >> >> Thanks >> Katherine >> >> >> On Thu, Dec 12, 2013 at 12:06 PM, > > wrote: >> >> ? ? Hei Paul, >> ? ? I tried your example and I get just at the beginning an error. See >> ? ? the attached file. >> >> ? ? Thanks, >> ? ? Barak >> >> ? ? On 12/11/2013 02:51 AM, nek5000-users at lists.mcs.anl.__gov >> ? ? wrote: >> >> >> ? ? ? ? Hi, >> >> ? ? ? ? I've added a Lagrangian particle tracking example --- >> >> ? ? ? ? ? ? examples/hemi >> >> ? ? ? ? look at hemi.usr. >> >> ? ? ? ? It produces a sequence of files with particle positions and >> ? ? ? ? a matlab script is provided for viewing.? As soon as I have >> ? ? ? ? a chance I'll also develop a script for visit. >> >> ? ? ? ? Paul >> >> >> ? ? ? ? ----- Original Message ----- >> ? ? ? ? From: nek5000-users at lists.mcs.anl.__gov >> ? ? ? ? >> ? ? ? ? To: nek5000-users at lists.mcs.anl.__gov >> ? ? ? ? >> ? ? ? ? Sent: Tuesday, December 10, 2013 4:25:19 PM >> ? ? ? ? Subject: Re: [Nek5000-users] Lagrangian particle tracking >> >> ? ? ? ? On 12/10/2013 03:27 PM, nek5000-users at lists.mcs.anl.__gov >> ? ? ? ? wrote: >> >> ? ? ? ? ? ? Le 10/12/2013 13:00, nek5000-users at lists.mcs.anl.__gov >> ? ? ? ? ? ? a ?crit >> >> >> >> ? ? ? ? ? ? Hello, >> >> ? ? ? ? ? ? ? ? What do you want to known about Lagrangian Particle >> ? ? ? ? ? ? Tracking ? >> >> >> >> ? ? ? ? Hi Anne, >> ? ? ? ? I would like to perform some Lagrangian particle simulation to to >> ? ? ? ? compute the component of the velocity field or vorticity at the >> ? ? ? ? particle. Do you have example for such computation as described >> ? ? ? ? in the >> ? ? ? ? webpage: >> ? ? ? ? http://nek5000.mcs.anl.gov/__index.php/Data_processing___example >> ? ? ? ? >> ? ? ? ? Thanks, >> >> ? ? ? ? Barak >> >> >> ? ? ? ? ? ? Anne Tani?re >> >> >> ? ? ? ? ? ? ? ? Hi >> ? ? ? ? ? ? ? ? I am interested to know if there is an example for the >> ? ? ? ? ? ? ? ? Lagrangian >> ? ? ? ? ? ? ? ? particle tracking >> ? ? ? ? ? ? ? ? as described in >> ? ? ? ? ? ? ? ? >> http://nek5000.mcs.anl.gov/__index.php/Data_processing___example >> ? ? ? ? ? ? ? ? >> >> ? ? ? ? ? ? ? ? . >> >> ? ? ? ? ? ? ? ? Thanks, >> ? ? ? ? ? ? ? ? Barak Galanti >> >> >> >> ? ? ? ? ? ? ? ? _________________________________________________ >> ? ? ? ? ? ? ? ? Nek5000-users mailing list >> ? ? ? ? ? ? ? ? Nek5000-users at lists.mcs.anl.__gov >> ? ? ? ? ? ? ? ? >> ? ? ? ? ? ? ? ? >> https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users >> ? ? ? ? ? ? ? ? >> >> >> >> >> ? ? ? ? ? ? -- >> ? ? ? ? ? ? Pr. Anne Tani?re, Lorraine University >> ? ? ? ? ? ? Nouvel email:anne.taniere at univ-__lorraine.fr >> ? ? ? ? ? ? >> ? ? ? ? ? ? Responsable des stages 5A, MFE ESSTIN >> ? ? ? ? ? ? tel : 03.83.68.50.83 >> >> >> >> ? ? ? ? ? ? _________________________________________________ >> ? ? ? ? ? ? Nek5000-users mailing list >> ? ? ? ? ? ? Nek5000-users at lists.mcs.anl.__gov >> ? ? ? ? ? ? >> ? ? ? ? ? ? https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users >> ? ? ? ? ? ? >> >> >> ? ? ? ? _________________________________________________ >> ? ? ? ? Nek5000-users mailing list >> ? ? ? ? Nek5000-users at lists.mcs.anl.__gov >> ? ? ? ? >> ? ? ? ? https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users >> ? ? ? ? >> ? ? ? ? _________________________________________________ >> ? ? ? ? Nek5000-users mailing list >> ? ? ? ? Nek5000-users at lists.mcs.anl.__gov >> ? ? ? ? >> ? ? ? ? https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users >> ? ? ? ? >> >> >> >> ? ? _______________________________________________ >> ? ? Nek5000-users mailing list >> ? ? Nek5000-users at lists.mcs.anl.gov >> >> ? ? https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.govhttps://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/gif Size: 450 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Fri Dec 13 12:01:28 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 13 Dec 2013 12:01:28 -0600 (CST) Subject: [Nek5000-users] Lagrangian particle tracking In-Reply-To: References: Message-ID: Yes - it could matter. The question is, how would you assess this, because the trajectories are chaotic... Probably it won't hurt to crank the tolerance down. With the projection schemes that we have the impact on pressure iteration is generally minimal. Paul On Fri, 13 Dec 2013, nek5000-users at lists.mcs.anl.gov wrote: > Hi Paul, > It helped a lot. But let me insist on the question of accuracy. If the > problem is well resolved (and spectrally accurate) then the divergence > error could matter. No? > I am interested to simulate turbulent flows so, this is the reason why > I am concerning about this issue. > Thanks again and have a nice weekend. > Barak > > Quoting nek5000-users at lists.mcs.anl.gov: >> Hi Barak, >> >> I have just a bit of time but will try to give you some quick answers to >> start. >> >> Interpolation is spectral. >> >> Decreasing div error simply sets the iteration tolerance tighter --- >> meaning that the _discrete_ system is solved to a tighter tolerance >> (i.e., closer to machine precision).?? ??However, it does not mean that >> the divergence is necessarily smaller, since there is also a >> discretization >> error associated with the fact that you are solving the discretized >> problem >> and not the continuous one.?? ??Discretization error can be reduced by >> increasing lx1 or the number of elements. >> >> If your problem is nondimensionalized in terms of convective timescales, >> I find div=1.e-6 is generally adequate (except, say, for certain >> stability problems, which tend to be very sensitive).?? If you are working >> in physical units, I would suggest set div=0 and tolrel = 0.01 ---- this >> will automatically choose tolerances for you.?? (It tends to be a bit more >> conservative than the 1.e-6 value that I suggest above.) >> >> There is a moving boundary example in the peristaltic flow example >> (/peris) >> At present, I don't have any falling body examples.?? Such a case is >> either >> easy or very hard, depending on the flow domain. >> >> hth, >> >> Paul >> >> >> ----- Original Message ----- >> From: nek5000-users at lists.mcs.anl.gov >> To: nek5000-users at lists.mcs.anl.gov >> Sent: Friday, December 13, 2013 3:44:49 AM >> Subject: Re: [Nek5000-users] Lagrangian particle tracking >> >> Hi Katherine, >> >> I reinstalled the new version (981) and indeed the code is running. I am >> going to check now the results. >> >> In previous messages I asked: >> 1. Is the used interpolation spectral? >> 2. When I decrease the desired divergence error, how does it increase >> the computation time? >> 3. Are there examples for moving solid bodies or boundaries? >> >> Many thanks. >> Barak >> >> On 12/12/2013 10:14 PM, nek5000-users at lists.mcs.anl.gov wrote: > Hi >> Barak, >>> >>> I believe your error is a result of a compiler specific update.?? I have >>> updated the Nek source code to hopefully address this issue.?? Please >>> update your code and let me know if the problem is not resolved. >>> >>> Thanks >>> Katherine >>> >>> >>> On Thu, Dec 12, 2013 at 12:06 PM, >> > wrote: >>> >>> ?? ?? Hei Paul, >>> ?? ?? I tried your example and I get just at the beginning an error. See >>> ?? ?? the attached file. >>> >>> ?? ?? Thanks, >>> ?? ?? Barak >>> >>> ?? ?? On 12/11/2013 02:51 AM, nek5000-users at lists.mcs.anl.__gov >>> ?? ?? wrote: >>> >>> >>> ?? ?? ?? ?? Hi, >>> >>> ?? ?? ?? ?? I've added a Lagrangian particle tracking example --- >>> >>> ?? ?? ?? ?? ?? ?? examples/hemi >>> >>> ?? ?? ?? ?? look at hemi.usr. >>> >>> ?? ?? ?? ?? It produces a sequence of files with particle positions and >>> ?? ?? ?? ?? a matlab script is provided for viewing.?? As soon as I have >>> ?? ?? ?? ?? a chance I'll also develop a script for visit. >>> >>> ?? ?? ?? ?? Paul >>> >>> >>> ?? ?? ?? ?? ----- Original Message ----- >>> ?? ?? ?? ?? From: nek5000-users at lists.mcs.anl.__gov >>> ?? ?? ?? ?? >>> ?? ?? ?? ?? To: nek5000-users at lists.mcs.anl.__gov >>> ?? ?? ?? ?? >>> ?? ?? ?? ?? Sent: Tuesday, December 10, 2013 4:25:19 PM >>> ?? ?? ?? ?? Subject: Re: [Nek5000-users] Lagrangian particle tracking >>> >>> ?? ?? ?? ?? On 12/10/2013 03:27 PM, nek5000-users at lists.mcs.anl.__gov >>> ?? ?? ?? ?? wrote: >>> >>> ?? ?? ?? ?? ?? ?? Le 10/12/2013 13:00, nek5000-users at lists.mcs.anl.__gov >>> ?? ?? ?? ?? ?? ?? a ??crit >>> >>> >>> >>> ?? ?? ?? ?? ?? ?? Hello, >>> >>> ?? ?? ?? ?? ?? ?? ?? ?? What do you want to known about Lagrangian >>> Particle >>> ?? ?? ?? ?? ?? ?? Tracking ? >>> >>> >>> >>> ?? ?? ?? ?? Hi Anne, >>> ?? ?? ?? ?? I would like to perform some Lagrangian particle simulation >>> to to >>> ?? ?? ?? ?? compute the component of the velocity field or vorticity at >>> the >>> ?? ?? ?? ?? particle. Do you have example for such computation as >>> described >>> ?? ?? ?? ?? in the >>> ?? ?? ?? ?? webpage: >>> ?? ?? ?? ?? >>> http://nek5000.mcs.anl.gov/__index.php/Data_processing___example >>> ?? ?? ?? ?? >>> >>> ?? ?? ?? ?? Thanks, >>> >>> ?? ?? ?? ?? Barak >>> >>> >>> ?? ?? ?? ?? ?? ?? Anne Tani??re >>> >>> >>> ?? ?? ?? ?? ?? ?? ?? ?? Hi >>> ?? ?? ?? ?? ?? ?? ?? ?? I am interested to know if there is an example >>> for the >>> ?? ?? ?? ?? ?? ?? ?? ?? Lagrangian >>> ?? ?? ?? ?? ?? ?? ?? ?? particle tracking >>> ?? ?? ?? ?? ?? ?? ?? ?? as described in >>> ?? ?? ?? ?? ?? ?? ?? ?? >>> http://nek5000.mcs.anl.gov/__index.php/Data_processing___example >>> ?? ?? ?? ?? ?? ?? ?? ?? >>> >>> ?? ?? ?? ?? ?? ?? ?? ?? . >>> >>> ?? ?? ?? ?? ?? ?? ?? ?? Thanks, >>> ?? ?? ?? ?? ?? ?? ?? ?? Barak Galanti >>> >>> >>> >>> ?? ?? ?? ?? ?? ?? ?? ?? >>> _________________________________________________ >>> ?? ?? ?? ?? ?? ?? ?? ?? Nek5000-users mailing list >>> ?? ?? ?? ?? ?? ?? ?? ?? Nek5000-users at lists.mcs.anl.__gov >>> ?? ?? ?? ?? ?? ?? ?? ?? >>> ?? ?? ?? ?? ?? ?? ?? ?? >>> https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users >>> ?? ?? ?? ?? ?? ?? ?? ?? >>> >>> >>> >>> >>> ?? ?? ?? ?? ?? ?? -- >>> ?? ?? ?? ?? ?? ?? Pr. Anne Tani??re, Lorraine University >>> ?? ?? ?? ?? ?? ?? Nouvel email:anne.taniere at univ-__lorraine.fr >>> ?? ?? ?? ?? ?? ?? >>> ?? ?? ?? ?? ?? ?? Responsable des stages 5A, MFE ESSTIN >>> ?? ?? ?? ?? ?? ?? tel : 03.83.68.50.83 >>> >>> >>> >>> ?? ?? ?? ?? ?? ?? _________________________________________________ >>> ?? ?? ?? ?? ?? ?? Nek5000-users mailing list >>> ?? ?? ?? ?? ?? ?? Nek5000-users at lists.mcs.anl.__gov >>> ?? ?? ?? ?? ?? ?? >>> ?? ?? ?? ?? ?? ?? >>> https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users >>> ?? ?? ?? ?? ?? ?? >>> >>> >>> >>> ?? ?? ?? ?? _________________________________________________ >>> ?? ?? ?? ?? Nek5000-users mailing list >>> ?? ?? ?? ?? Nek5000-users at lists.mcs.anl.__gov >>> ?? ?? ?? ?? >>> ?? ?? ?? ?? https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users >>> ?? ?? ?? ?? >>> ?? ?? ?? ?? _________________________________________________ >>> ?? ?? ?? ?? Nek5000-users mailing list >>> ?? ?? ?? ?? Nek5000-users at lists.mcs.anl.__gov >>> ?? ?? ?? ?? >>> ?? ?? ?? ?? https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users >>> ?? ?? ?? ?? >>> >>> >>> >>> ?? ?? _______________________________________________ >>> ?? ?? Nek5000-users mailing list >>> ?? ?? Nek5000-users at lists.mcs.anl.gov >>> >>> ?? ?? https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >>> >>> >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.govhttps://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Fri Dec 13 13:07:41 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 13 Dec 2013 14:07:41 -0500 Subject: [Nek5000-users] problem with interpolation by hpts Message-ID: Hi, I have a problem with hpts() function to interpolating data. I was using hpts() function without any problem in userchk and by input it was giving me the interpolation, but after some days I don't what change I did, whatever I interpolate now it just gives me multiplication of certain points(like in one case is 107 points and in other it is 90), I think there is some problems with setting parameters on SIZE, below is my SIZE file for one of my cases which I can just get interpolation with multiplication of 107 points (if I have less than 107 points in hpts.in, it just gives me nothing in htps.out!!): C Dimension file to be included C C HCUBE array dimensions C parameter (ldim=3) parameter (lx1=6,ly1=lx1,lz1=lx1,lelt=410,lelv=lelt) parameter (lxd=10,lyd=lxd,lzd=lxd) parameter (lelx=1,lely=1,lelz=1) parameter (lzl=3 + 2*(ldim-3)) parameter (lx2=lx1-2) parameter (ly2=ly1-2) parameter (lz2=lz1-2) parameter (lx3=lx1) parameter (ly3=ly1) parameter (lz3=lz1) parameter (lp = 512) parameter (lelg = 16000) c c parameter (lpelv=lelv,lpelt=lelt,lpert=3) ! perturbation c parameter (lpx1=lx1,lpy1=ly1,lpz1=lz1) ! array sizes c parameter (lpx2=lx2,lpy2=ly2,lpz2=lz2) c parameter (lpelv=1,lpelt=1,lpert=1) ! perturbation parameter (lpx1=1,lpy1=1,lpz1=1) ! array sizes parameter (lpx2=1,lpy2=1,lpz2=1) c c parameter (lbelv=lelv,lbelt=lelt) ! MHD c parameter (lbx1=lx1,lby1=ly1,lbz1=lz1) ! array sizes c parameter (lbx2=lx2,lby2=ly2,lbz2=lz2) c parameter (lbelv=1,lbelt=1) ! MHD parameter (lbx1=1,lby1=1,lbz1=1) ! array sizes parameter (lbx2=1,lby2=1,lbz2=1) C LX1M=LX1 when there are moving meshes; =1 otherwise parameter (lx1m=1,ly1m=1,lz1m=1) parameter (ldimt= 2) ! 3 passive scalars + T parameter (ldimt1=ldimt+1) parameter (ldimt3=ldimt+3) c c Note: In the new code, LELGEC should be about sqrt(LELG) c PARAMETER (LELGEC = 1) PARAMETER (LXYZ2 = 1) PARAMETER (LXZ21 = 1) PARAMETER (LMAXV=LX1*LY1*LZ1*LELV) PARAMETER (LMAXT=LX1*LY1*LZ1*LELT) PARAMETER (LMAXP=LX2*LY2*LZ2*LELV) PARAMETER (LXZ=LX1*LZ1) PARAMETER (LORDER=3) PARAMETER (MAXOBJ=4,MAXMBR=LELT*6) PARAMETER (lhis=200) ! # of pts a proc reads from hpts.in ! Note: lhis*np > npoints in hpts.in C C Common Block Dimensions C PARAMETER (LCTMP0 =2*LX1*LY1*LZ1*LELT) PARAMETER (LCTMP1 =4*LX1*LY1*LZ1*LELT) C C The parameter LVEC controls whether an additional 42 field arrays C are required for Steady State Solutions. If you are not using C Steady State, it is recommended that LVEC=1. C PARAMETER (LVEC=1) C C Uzawa projection array dimensions C parameter (mxprev = 20) parameter (lgmres = 30) C C Split projection array dimensions C parameter(lmvec = 1) parameter(lsvec = 1) parameter(lstore=lmvec*lsvec) c c NONCONFORMING STUFF c parameter (maxmor = lelt) C C Array dimensions C COMMON/DIMN/NELV,NELT,NX1,NY1,NZ1,NX2,NY2,NZ2 $,NX3,NY3,NZ3,NDIM,NFIELD,NPERT,NID $,NXD,NYD,NZD c automatically added by makenek parameter(lxo = lx1) ! max output grid size (lxo>=lx1) c automatically added by makenek parameter(lpart = 1 ) ! max number of particles c automatically added by makenek integer ax1,ay1,az1,ax2,ay2,az2 parameter (ax1=lx1,ay1=ly1,az1=lz1,ax2=lx2,ay2=ly2,az2=lz2) ! running averages c automatically added by makenek parameter (lxs=1,lys=lxs,lzs=(lxs-1)*(ldim-2)+1) !New Pressure Preconditioner c automatically added by makenek parameter (lfdm=0) ! == 1 for fast diagonalization method Is anyone has idea what is the problem in this case?! Thanks, Ami -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sun Dec 15 16:14:22 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 16 Dec 2013 00:14:22 +0200 Subject: [Nek5000-users] turbulent 3d box In-Reply-To: References: Message-ID: Dear nek's, I would like to run the following problem: a 3D periodic box, small viscosity and the following forcing: fx=cos(y)+sin(z) fy=cos(z)+sin(x) fz=cos(x)+sin(y) Do you have a similar example? Many thanks, Barak From nek5000-users at lists.mcs.anl.gov Sun Dec 15 20:07:15 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 15 Dec 2013 20:07:15 -0600 (CST) Subject: [Nek5000-users] turbulent 3d box In-Reply-To: Message-ID: Hi Barak, Just take the box file from turbChannel and set nelx nely nelz to (say) -8 -8 -8 with periodic BCs P ,P ,P ,P ,P , Then, use a blank .usr file and set ffx fry ffz to be the formulas you have below in userf() in the .usr file. Finally, add the following to usrdat2() a=0 b=2*pi call rescale_x(xm1,a,b) call rescale_x(ym1,a,b) call rescale_x(zm1,a,b) which will put your box on [0,2pi]^3. Paul ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Sunday, December 15, 2013 4:14:22 PM Subject: [Nek5000-users] turbulent 3d box Dear nek's, I would like to run the following problem: a 3D periodic box, small viscosity and the following forcing: fx=cos(y)+sin(z) fy=cos(z)+sin(x) fz=cos(x)+sin(y) Do you have a similar example? Many thanks, Barak _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Mon Dec 16 02:31:46 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 16 Dec 2013 10:31:46 +0200 Subject: [Nek5000-users] turbulent 3d box In-Reply-To: References: Message-ID: Hi Paul, It seems that many more things are missing. Here is the compilation errors: mpicc -c? -O2 -DPTRSIZE8 -DMPI -DLONGINT8 -DUNDERSCORE -DGLOBAL_LONG_LONG? -DPREFIX=jl_ /home/galanti/COMPUTING/NEK5000/nek5_svn/trunk/nek/jl/xxt.c -o obj/jl_xxt.o mpicc -c? -O2 -DPTRSIZE8 -DMPI -DLONGINT8 -DUNDERSCORE -DGLOBAL_LONG_LONG? -DPREFIX=jl_ /home/galanti/COMPUTING/NEK5000/nek5_svn/trunk/nek/jl/fcrs.c -o obj/jl_fcrs.o mpif77 -c? -O2 -fdefault-real-8 -fdefault-double-8 -x f77-cpp-input -DPTRSIZE8 -DMPI -DLONGINT8 -DUNDERSCORE -DGLOBAL_LONG_LONG -I/home/galanti/COMPUTING/NEK5000/nek5_svn/TEST-examples/turbBox -I/home/galanti/COMPUTING/NEK5000/nek5_svn/trunk/nek -I./ /home/galanti/COMPUTING/NEK5000/nek5_svn/TEST-examples/turbBox/turbBox.f??? -o obj/turbBox.o mpif77 -o nek5000? obj/turbBox.o obj/drive.o obj/drive1.o obj/drive2.o obj/plan4.o obj/bdry.o obj/coef.o obj/conduct.o obj/connect1.o obj/connect2.o obj/dssum.o obj/edgec.o obj/eigsolv.o obj/gauss.o obj/genxyz.o obj/navier1.o obj/makeq.o obj/navier0.o obj/navier2.o obj/navier3.o obj/navier4.o obj/prepost.o obj/speclib.o obj/map2.o obj/turb.o obj/mvmesh.o obj/ic.o obj/ssolv.o obj/planx.o obj/math.o obj/mxm_wrapper.o obj/hmholtz.o obj/gfdm_par.o obj/gfdm_op.o obj/gfdm_solve.o obj/subs1.o obj/subs2.o obj/genbox.o obj/gmres.o obj/hsmg.o obj/convect.o obj/induct.o obj/perturb.o obj/navier5.o obj/navier6.o obj/navier7.o obj/navier8.o obj/fast3d.o obj/fasts.o obj/calcz.o obj/byte.o obj/chelpers.o obj/byte_mpi.o obj/postpro.o obj/cvode_driver.o obj/nek_comm.o obj/init_plugin.o obj/setprop.o obj/qthermal.o obj/cvode_aux.o obj/makeq_aux.o obj/papi.o obj/ssygv.o obj/dsygv.o obj/nek_in_situ.o obj/mxm_std.o obj/blas.o obj/comm_mpi.o obj/singlmesh.o obj/jl_gs.o obj/jl_sort.o obj/jl_sarray_transfer.o obj/jl_sarray_sort.o obj/jl_gs_local.o obj/jl_crystal.o obj/jl_comm.o obj/jl_tensor.o obj/jl_fail.o obj/jl_fcrystal.o obj/jl_findpts.o obj/jl_findpts_local.o obj/jl_obbox.o obj/jl_poly.o obj/jl_lob_bnd.o obj/jl_findpts_el_3.o obj/jl_findpts_el_2.o obj/jl_sparse_cholesky.o obj/jl_xxt.o obj/jl_fcrs.o obj/drive1.o: In function `nek_init_': drive1.f:(.text+0x48b): undefined reference to `usrdat_' drive1.f:(.text+0x578): undefined reference to `usrdat3_' drive1.f:(.text+0x5b5): undefined reference to `userchk_' obj/drive1.o: In function `nek_solve_': drive1.f:(.text+0xc7e): undefined reference to `userchk_' drive1.f:(.text+0xcf7): undefined reference to `userchk_' obj/bdry.o: In function `faceiv_': bdry.f:(.text+0x2a5f): undefined reference to `userbc_' bdry.f:(.text+0x2e74): undefined reference to `userbc_' bdry.f:(.text+0x2f53): undefined reference to `userbc_' bdry.f:(.text+0x309f): undefined reference to `userbc_' bdry.f:(.text+0x31d9): undefined reference to `userbc_' obj/bdry.o:bdry.f:(.text+0x3352): more undefined references to `userbc_' follow obj/conduct.o: In function `nekuq_': conduct.f:(.text+0xdcf): undefined reference to `userq_' obj/ic.o: In function `nekuic_': ic.f:(.text+0x6a6): undefined reference to `useric_' ic.f:(.text+0x980): undefined reference to `useric_' ic.f:(.text+0xad0): undefined reference to `useric_' obj/ssolv.o: In function `gostep_': ssolv.f:(.text+0x1954): undefined reference to `userchk_' obj/ssolv.o: In function `go1step_': ssolv.f:(.text+0x2424): undefined reference to `userchk_' obj/subs1.o: In function `nekuvp_': subs1.f:(.text+0x90c): undefined reference to `uservp_' collect2: error: ld returned 1 exit status make: *** [nek5000] Error 1 Attached the .usr and .box files which I used. What about the turBox.f file ? All the best, Barak Quoting nek5000-users at lists.mcs.anl.gov: > Hi Barak, > > Just take the box file from turbChannel > and set nelx nely nelz to (say) -8 -8 -8 > with periodic BCs? P? ,P? ,P? ,P? ,P? , > > Then, use a blank .usr file and set ffx fry ffz to be the > formulas you have below in userf() in the .usr file. > > Finally, add the following to usrdat2() > > ? ? ?a=0 > ? ? ?b=2*pi > ? ? ?call rescale_x(xm1,a,b) > ? ? ?call rescale_x(ym1,a,b) > ? ? ?call rescale_x(zm1,a,b) > > which will put your box on [0,2pi]^3. > > Paul > > > ----- Original Message ----- > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Sent: Sunday, December 15, 2013 4:14:22 PM > Subject: [Nek5000-users] turbulent 3d box > > Dear nek's, > I would like to run the following problem: > a 3D periodic box, small viscosity and the following forcing: > > fx=cos(y)+sin(z) > fy=cos(z)+sin(x) > fz=cos(x)+sin(y) > > Do you have a similar example? > > Many thanks, > Barak > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.govhttps://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: turbBox.box Type: application/octet-stream Size: 1011 bytes Desc: turbBox.box URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: turbBox.usr Type: application/octet-stream Size: 583 bytes Desc: turbBox.usr URL: From nek5000-users at lists.mcs.anl.gov Mon Dec 16 05:05:46 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 16 Dec 2013 12:05:46 +0100 Subject: [Nek5000-users] Magnetic boundary conditions (especially (quasi) vacuum conditions) In-Reply-To: References: Message-ID: Hello Aleks, thanks for your reply, that's good news. I will try to run some test cases with simple geometries and might come back to you with further questions. Thanks again, Jan From nek5000-users at lists.mcs.anl.gov Mon Dec 16 11:37:45 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 16 Dec 2013 17:37:45 +0000 Subject: [Nek5000-users] turbulent 3d box In-Reply-To: References: , Message-ID: Sorry - by "blank" .usr file, I meant one of the zero.usr files from nek5_svn/trunk/nek ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Monday, December 16, 2013 2:31 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] turbulent 3d box Hi Paul, It seems that many more things are missing. Here is the compilation errors: mpicc -c -O2 -DPTRSIZE8 -DMPI -DLONGINT8 -DUNDERSCORE -DGLOBAL_LONG_LONG -DPREFIX=jl_ /home/galanti/COMPUTING/NEK5000/nek5_svn/trunk/nek/jl/xxt.c -o obj/jl_xxt.o mpicc -c -O2 -DPTRSIZE8 -DMPI -DLONGINT8 -DUNDERSCORE -DGLOBAL_LONG_LONG -DPREFIX=jl_ /home/galanti/COMPUTING/NEK5000/nek5_svn/trunk/nek/jl/fcrs.c -o obj/jl_fcrs.o mpif77 -c -O2 -fdefault-real-8 -fdefault-double-8 -x f77-cpp-input -DPTRSIZE8 -DMPI -DLONGINT8 -DUNDERSCORE -DGLOBAL_LONG_LONG -I/home/galanti/COMPUTING/NEK5000/nek5_svn/TEST-examples/turbBox -I/home/galanti/COMPUTING/NEK5000/nek5_svn/trunk/nek -I./ /home/galanti/COMPUTING/NEK5000/nek5_svn/TEST-examples/turbBox/turbBox.f -o obj/turbBox.o mpif77 -o nek5000 obj/turbBox.o obj/drive.o obj/drive1.o obj/drive2.o obj/plan4.o obj/bdry.o obj/coef.o obj/conduct.o obj/connect1.o obj/connect2.o obj/dssum.o obj/edgec.o obj/eigsolv.o obj/gauss.o obj/genxyz.o obj/navier1.o obj/makeq.o obj/navier0.o obj/navier2.o obj/navier3.o obj/navier4.o obj/prepost.o obj/speclib.o obj/map2.o obj/turb.o obj/mvmesh.o obj/ic.o obj/ssolv.o obj/planx.o obj/math.o obj/mxm_wrapper.o obj/hmholtz.o obj/gfdm_par.o obj/gfdm_op.o obj/gfdm_solve.o obj/subs1.o obj/subs2.o obj/genbox.o obj/gmres.o obj/hsmg.o obj/convect.o obj/induct.o obj/perturb.o obj/navier5.o obj/navier6.o obj/navier7.o obj/navier8.o obj/fast3d.o obj/fasts.o obj/calcz.o obj/byte.o obj/chelpers.o obj/byte_mpi.o obj/postpro.o obj/cvode_driver.o obj/nek_comm.o obj/init_plugin.o obj/setprop.o obj/qthermal.o obj/cvode_aux.o obj/makeq_aux.o obj/papi.o obj/ssygv.o obj/dsygv.o obj/nek_in_situ.o obj/mxm_std.o obj/blas.o obj/comm_mpi.o obj/singlmesh.o obj/jl_gs.o obj/jl_sort.o obj/jl_sarray_transfer.o obj/jl_sarray_sort.o obj/jl_gs_local.o obj/jl_crystal.o obj/jl_comm.o obj/jl_tensor.o obj/jl_fail.o obj/jl_fcrystal.o obj/jl_findpts.o obj/jl_findpts_local.o obj/jl_obbox.o obj/jl_poly.o obj/jl_lob_bnd.o obj/jl_findpts_el_3.o obj/jl_findpts_el_2.o obj/jl_sparse_cholesky.o obj/jl_xxt.o obj/jl_fcrs.o obj/drive1.o: In function `nek_init_': drive1.f:(.text+0x48b): undefined reference to `usrdat_' drive1.f:(.text+0x578): undefined reference to `usrdat3_' drive1.f:(.text+0x5b5): undefined reference to `userchk_' obj/drive1.o: In function `nek_solve_': drive1.f:(.text+0xc7e): undefined reference to `userchk_' drive1.f:(.text+0xcf7): undefined reference to `userchk_' obj/bdry.o: In function `faceiv_': bdry.f:(.text+0x2a5f): undefined reference to `userbc_' bdry.f:(.text+0x2e74): undefined reference to `userbc_' bdry.f:(.text+0x2f53): undefined reference to `userbc_' bdry.f:(.text+0x309f): undefined reference to `userbc_' bdry.f:(.text+0x31d9): undefined reference to `userbc_' obj/bdry.o:bdry.f:(.text+0x3352): more undefined references to `userbc_' follow obj/conduct.o: In function `nekuq_': conduct.f:(.text+0xdcf): undefined reference to `userq_' obj/ic.o: In function `nekuic_': ic.f:(.text+0x6a6): undefined reference to `useric_' ic.f:(.text+0x980): undefined reference to `useric_' ic.f:(.text+0xad0): undefined reference to `useric_' obj/ssolv.o: In function `gostep_': ssolv.f:(.text+0x1954): undefined reference to `userchk_' obj/ssolv.o: In function `go1step_': ssolv.f:(.text+0x2424): undefined reference to `userchk_' obj/subs1.o: In function `nekuvp_': subs1.f:(.text+0x90c): undefined reference to `uservp_' collect2: error: ld returned 1 exit status make: *** [nek5000] Error 1 Attached the .usr and .box files which I used. What about the turBox.f file ? All the best, Barak Quoting nek5000-users at lists.mcs.anl.gov: Hi Barak, Just take the box file from turbChannel and set nelx nely nelz to (say) -8 -8 -8 with periodic BCs P ,P ,P ,P ,P , Then, use a blank .usr file and set ffx fry ffz to be the formulas you have below in userf() in the .usr file. Finally, add the following to usrdat2() a=0 b=2*pi call rescale_x(xm1,a,b) call rescale_x(ym1,a,b) call rescale_x(zm1,a,b) which will put your box on [0,2pi]^3. Paul ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Sunday, December 15, 2013 4:14:22 PM Subject: [Nek5000-users] turbulent 3d box Dear nek's, I would like to run the following problem: a 3D periodic box, small viscosity and the following forcing: fx=cos(y)+sin(z) fy=cos(z)+sin(x) fz=cos(x)+sin(y) Do you have a similar example? Many thanks, Barak _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.govhttps://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Dec 17 07:04:30 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 17 Dec 2013 07:04:30 -0600 Subject: [Nek5000-users] problem with interpolation by hpts In-Reply-To: References: Message-ID: Hi Ami, As long as lhis times the number of processors is greater than your total number of points (as the comment in the SIZE file suggests), then the SIZE file shouldn't cause any issues. How many total points are you trying to interpolate? If your hpts.in file is not too large, could you post that (as well as the relevant portion of your .usr file where you call the hpts routine) - Josh On Fri, Dec 13, 2013 at 1:07 PM, wrote: > Hi, > > I have a problem with hpts() function to interpolating data. I was using > hpts() function without any problem in userchk and by input it was giving > me the interpolation, but after some days I don't what change I did, > whatever I interpolate now it just gives me multiplication of certain > points(like in one case is 107 points and in other it is 90), I think there > is some problems with setting parameters on SIZE, below is my SIZE file for > one of my cases which I can just get interpolation with multiplication of > 107 points (if I have less than 107 points in hpts.in, it just gives me > nothing in htps.out!!): > > C Dimension file to be included > C > C HCUBE array dimensions > C > parameter (ldim=3) > parameter (lx1=6,ly1=lx1,lz1=lx1,lelt=410,lelv=lelt) > parameter (lxd=10,lyd=lxd,lzd=lxd) > parameter (lelx=1,lely=1,lelz=1) > > parameter (lzl=3 + 2*(ldim-3)) > > parameter (lx2=lx1-2) > parameter (ly2=ly1-2) > parameter (lz2=lz1-2) > parameter (lx3=lx1) > parameter (ly3=ly1) > parameter (lz3=lz1) > > parameter (lp = 512) > parameter (lelg = 16000) > c > c parameter (lpelv=lelv,lpelt=lelt,lpert=3) ! perturbation > c parameter (lpx1=lx1,lpy1=ly1,lpz1=lz1) ! array sizes > c parameter (lpx2=lx2,lpy2=ly2,lpz2=lz2) > c > parameter (lpelv=1,lpelt=1,lpert=1) ! perturbation > parameter (lpx1=1,lpy1=1,lpz1=1) ! array sizes > parameter (lpx2=1,lpy2=1,lpz2=1) > c > c parameter (lbelv=lelv,lbelt=lelt) ! MHD > c parameter (lbx1=lx1,lby1=ly1,lbz1=lz1) ! array sizes > c parameter (lbx2=lx2,lby2=ly2,lbz2=lz2) > c > parameter (lbelv=1,lbelt=1) ! MHD > parameter (lbx1=1,lby1=1,lbz1=1) ! array sizes > parameter (lbx2=1,lby2=1,lbz2=1) > > C LX1M=LX1 when there are moving meshes; =1 otherwise > parameter (lx1m=1,ly1m=1,lz1m=1) > parameter (ldimt= 2) ! 3 passive scalars + T > parameter (ldimt1=ldimt+1) > parameter (ldimt3=ldimt+3) > c > c Note: In the new code, LELGEC should be about sqrt(LELG) > c > PARAMETER (LELGEC = 1) > PARAMETER (LXYZ2 = 1) > PARAMETER (LXZ21 = 1) > > PARAMETER (LMAXV=LX1*LY1*LZ1*LELV) > PARAMETER (LMAXT=LX1*LY1*LZ1*LELT) > PARAMETER (LMAXP=LX2*LY2*LZ2*LELV) > PARAMETER (LXZ=LX1*LZ1) > PARAMETER (LORDER=3) > PARAMETER (MAXOBJ=4,MAXMBR=LELT*6) > PARAMETER (lhis=200) ! # of pts a proc reads from hpts.in > ! Note: lhis*np > npoints in hpts.in > C > C Common Block Dimensions > C > PARAMETER (LCTMP0 =2*LX1*LY1*LZ1*LELT) > PARAMETER (LCTMP1 =4*LX1*LY1*LZ1*LELT) > C > C The parameter LVEC controls whether an additional 42 field arrays > C are required for Steady State Solutions. If you are not using > C Steady State, it is recommended that LVEC=1. > C > PARAMETER (LVEC=1) > C > C Uzawa projection array dimensions > C > parameter (mxprev = 20) > parameter (lgmres = 30) > C > C Split projection array dimensions > C > parameter(lmvec = 1) > parameter(lsvec = 1) > parameter(lstore=lmvec*lsvec) > c > c NONCONFORMING STUFF > c > parameter (maxmor = lelt) > C > C Array dimensions > C > COMMON/DIMN/NELV,NELT,NX1,NY1,NZ1,NX2,NY2,NZ2 > $,NX3,NY3,NZ3,NDIM,NFIELD,NPERT,NID > $,NXD,NYD,NZD > > c automatically added by makenek > parameter(lxo = lx1) ! max output grid size (lxo>=lx1) > > c automatically added by makenek > parameter(lpart = 1 ) ! max number of particles > > c automatically added by makenek > integer ax1,ay1,az1,ax2,ay2,az2 > parameter (ax1=lx1,ay1=ly1,az1=lz1,ax2=lx2,ay2=ly2,az2=lz2) ! > running averages > > c automatically added by makenek > parameter (lxs=1,lys=lxs,lzs=(lxs-1)*(ldim-2)+1) !New Pressure > Preconditioner > > c automatically added by makenek > parameter (lfdm=0) ! == 1 for fast diagonalization method > > Is anyone has idea what is the problem in this case?! > > Thanks, > Ami > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -- Josh Camp "All that is necessary for the triumph of evil is that good men do nothing" -- Edmund Burke -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Dec 17 09:47:23 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 17 Dec 2013 10:47:23 -0500 Subject: [Nek5000-users] problem with interpolation by hpts In-Reply-To: References: Message-ID: H On Tue, Dec 17, 2013 at 8:04 AM, wrote: > Hi Ami, > > As long as lhis times the number of processors is greater than your total > number of points (as the comment in the SIZE file suggests), then the SIZE > file shouldn't cause any issues. > > How many total points are you trying to interpolate? If your hpts.infile is not too large, could you post that (as well as the relevant portion > of your .usr file where you call the hpts routine) > > - Josh > > > On Fri, Dec 13, 2013 at 1:07 PM, wrote: > >> Hi, >> >> I have a problem with hpts() function to interpolating data. I was using >> hpts() function without any problem in userchk and by input it was giving >> me the interpolation, but after some days I don't what change I did, >> whatever I interpolate now it just gives me multiplication of certain >> points(like in one case is 107 points and in other it is 90), I think there >> is some problems with setting parameters on SIZE, below is my SIZE file for >> one of my cases which I can just get interpolation with multiplication of >> 107 points (if I have less than 107 points in hpts.in, it just gives me >> nothing in htps.out!!): >> >> C Dimension file to be included >> C >> C HCUBE array dimensions >> C >> parameter (ldim=3) >> parameter (lx1=6,ly1=lx1,lz1=lx1,lelt=410,lelv=lelt) >> parameter (lxd=10,lyd=lxd,lzd=lxd) >> parameter (lelx=1,lely=1,lelz=1) >> >> parameter (lzl=3 + 2*(ldim-3)) >> >> parameter (lx2=lx1-2) >> parameter (ly2=ly1-2) >> parameter (lz2=lz1-2) >> parameter (lx3=lx1) >> parameter (ly3=ly1) >> parameter (lz3=lz1) >> >> parameter (lp = 512) >> parameter (lelg = 16000) >> c >> c parameter (lpelv=lelv,lpelt=lelt,lpert=3) ! perturbation >> c parameter (lpx1=lx1,lpy1=ly1,lpz1=lz1) ! array sizes >> c parameter (lpx2=lx2,lpy2=ly2,lpz2=lz2) >> c >> parameter (lpelv=1,lpelt=1,lpert=1) ! perturbation >> parameter (lpx1=1,lpy1=1,lpz1=1) ! array sizes >> parameter (lpx2=1,lpy2=1,lpz2=1) >> c >> c parameter (lbelv=lelv,lbelt=lelt) ! MHD >> c parameter (lbx1=lx1,lby1=ly1,lbz1=lz1) ! array sizes >> c parameter (lbx2=lx2,lby2=ly2,lbz2=lz2) >> c >> parameter (lbelv=1,lbelt=1) ! MHD >> parameter (lbx1=1,lby1=1,lbz1=1) ! array sizes >> parameter (lbx2=1,lby2=1,lbz2=1) >> >> C LX1M=LX1 when there are moving meshes; =1 otherwise >> parameter (lx1m=1,ly1m=1,lz1m=1) >> parameter (ldimt= 2) ! 3 passive scalars + T >> parameter (ldimt1=ldimt+1) >> parameter (ldimt3=ldimt+3) >> c >> c Note: In the new code, LELGEC should be about sqrt(LELG) >> c >> PARAMETER (LELGEC = 1) >> PARAMETER (LXYZ2 = 1) >> PARAMETER (LXZ21 = 1) >> >> PARAMETER (LMAXV=LX1*LY1*LZ1*LELV) >> PARAMETER (LMAXT=LX1*LY1*LZ1*LELT) >> PARAMETER (LMAXP=LX2*LY2*LZ2*LELV) >> PARAMETER (LXZ=LX1*LZ1) >> PARAMETER (LORDER=3) >> PARAMETER (MAXOBJ=4,MAXMBR=LELT*6) >> PARAMETER (lhis=200) ! # of pts a proc reads from hpts.in >> ! Note: lhis*np > npoints in hpts.in >> C >> C Common Block Dimensions >> C >> PARAMETER (LCTMP0 =2*LX1*LY1*LZ1*LELT) >> PARAMETER (LCTMP1 =4*LX1*LY1*LZ1*LELT) >> C >> C The parameter LVEC controls whether an additional 42 field arrays >> C are required for Steady State Solutions. If you are not using >> C Steady State, it is recommended that LVEC=1. >> C >> PARAMETER (LVEC=1) >> C >> C Uzawa projection array dimensions >> C >> parameter (mxprev = 20) >> parameter (lgmres = 30) >> C >> C Split projection array dimensions >> C >> parameter(lmvec = 1) >> parameter(lsvec = 1) >> parameter(lstore=lmvec*lsvec) >> c >> c NONCONFORMING STUFF >> c >> parameter (maxmor = lelt) >> C >> C Array dimensions >> C >> COMMON/DIMN/NELV,NELT,NX1,NY1,NZ1,NX2,NY2,NZ2 >> $,NX3,NY3,NZ3,NDIM,NFIELD,NPERT,NID >> $,NXD,NYD,NZD >> >> c automatically added by makenek >> parameter(lxo = lx1) ! max output grid size (lxo>=lx1) >> >> c automatically added by makenek >> parameter(lpart = 1 ) ! max number of particles >> >> c automatically added by makenek >> integer ax1,ay1,az1,ax2,ay2,az2 >> parameter (ax1=lx1,ay1=ly1,az1=lz1,ax2=lx2,ay2=ly2,az2=lz2) ! >> running averages >> >> c automatically added by makenek >> parameter (lxs=1,lys=lxs,lzs=(lxs-1)*(ldim-2)+1) !New Pressure >> Preconditioner >> >> c automatically added by makenek >> parameter (lfdm=0) ! == 1 for fast diagonalization method >> >> Is anyone has idea what is the problem in this case?! >> >> Thanks, >> Ami >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> > > > -- > Josh Camp > > "All that is necessary for the triumph of evil is that good men do > nothing" -- Edmund Burke > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Dec 17 10:00:22 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 17 Dec 2013 18:00:22 +0200 Subject: [Nek5000-users] turbulent 3d box In-Reply-To: References: , Message-ID: Hi Paul, It seems that something is really bad!! I guess it is with userf() (are x,y,z defined? they should be the coordinates along the Box axes). Attached please find the relevant files. Thanks, Barak Could you please look at the attached library. I added the image of the initial stage. Thanks, Barak On 12/16/2013 07:37 PM, nek5000-users at lists.mcs.anl.gov wrote: > > Sorry - by "blank" .usr file, I meant one of the zero.usr files from > > nek5_svn/trunk/nek > > > ------------------------------------------------------------------------ > *From:* nek5000-users-bounces at lists.mcs.anl.gov > [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of > nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] > *Sent:* Monday, December 16, 2013 2:31 AM > *To:* nek5000-users at lists.mcs.anl.gov > *Subject:* Re: [Nek5000-users] turbulent 3d box > > > Hi Paul, > It seems that many more things are missing. Here is the compilation errors: > > mpicc -c -O2 -DPTRSIZE8 -DMPI -DLONGINT8 -DUNDERSCORE > -DGLOBAL_LONG_LONG -DPREFIX=jl_ > /home/galanti/COMPUTING/NEK5000/nek5_svn/trunk/nek/jl/xxt.c -o obj/jl_xxt.o > mpicc -c -O2 -DPTRSIZE8 -DMPI -DLONGINT8 -DUNDERSCORE > -DGLOBAL_LONG_LONG -DPREFIX=jl_ > /home/galanti/COMPUTING/NEK5000/nek5_svn/trunk/nek/jl/fcrs.c -o > obj/jl_fcrs.o > mpif77 -c -O2 -fdefault-real-8 -fdefault-double-8 -x f77-cpp-input > -DPTRSIZE8 -DMPI -DLONGINT8 -DUNDERSCORE -DGLOBAL_LONG_LONG > -I/home/galanti/COMPUTING/NEK5000/nek5_svn/TEST-examples/turbBox > -I/home/galanti/COMPUTING/NEK5000/nek5_svn/trunk/nek -I./ > /home/galanti/COMPUTING/NEK5000/nek5_svn/TEST-examples/turbBox/turbBox.f > -o obj/turbBox.o > mpif77 -o nek5000 obj/turbBox.o obj/drive.o obj/drive1.o obj/drive2.o > obj/plan4.o obj/bdry.o obj/coef.o obj/conduct.o obj/connect1.o > obj/connect2.o obj/dssum.o obj/edgec.o obj/eigsolv.o obj/gauss.o > obj/genxyz.o obj/navier1.o obj/makeq.o obj/navier0.o obj/navier2.o > obj/navier3.o obj/navier4.o obj/prepost.o obj/speclib.o obj/map2.o > obj/turb.o obj/mvmesh.o obj/ic.o obj/ssolv.o obj/planx.o obj/math.o > obj/mxm_wrapper.o obj/hmholtz.o obj/gfdm_par.o obj/gfdm_op.o > obj/gfdm_solve.o obj/subs1.o obj/subs2.o obj/genbox.o obj/gmres.o > obj/hsmg.o obj/convect.o obj/induct.o obj/perturb.o obj/navier5.o > obj/navier6.o obj/navier7.o obj/navier8.o obj/fast3d.o obj/fasts.o > obj/calcz.o obj/byte.o obj/chelpers.o obj/byte_mpi.o obj/postpro.o > obj/cvode_driver.o obj/nek_comm.o obj/init_plugin.o obj/setprop.o > obj/qthermal.o obj/cvode_aux.o obj/makeq_aux.o obj/papi.o obj/ssygv.o > obj/dsygv.o obj/nek_in_situ.o obj/mxm_std.o obj/blas.o obj/comm_mpi.o > obj/singlmesh.o obj/jl_gs.o obj/jl_sort.o obj/jl_sarray_transfer.o > obj/jl_sarray_sort.o obj/jl_gs_local.o obj/jl_crystal.o obj/jl_comm.o > obj/jl_tensor.o obj/jl_fail.o obj/jl_fcrystal.o obj/jl_findpts.o > obj/jl_findpts_local.o obj/jl_obbox.o obj/jl_poly.o obj/jl_lob_bnd.o > obj/jl_findpts_el_3.o obj/jl_findpts_el_2.o obj/jl_sparse_cholesky.o > obj/jl_xxt.o obj/jl_fcrs.o > obj/drive1.o: In function `nek_init_': > drive1.f:(.text+0x48b): undefined reference to `usrdat_' > drive1.f:(.text+0x578): undefined reference to `usrdat3_' > drive1.f:(.text+0x5b5): undefined reference to `userchk_' > obj/drive1.o: In function `nek_solve_': > drive1.f:(.text+0xc7e): undefined reference to `userchk_' > drive1.f:(.text+0xcf7): undefined reference to `userchk_' > obj/bdry.o: In function `faceiv_': > bdry.f:(.text+0x2a5f): undefined reference to `userbc_' > bdry.f:(.text+0x2e74): undefined reference to `userbc_' > bdry.f:(.text+0x2f53): undefined reference to `userbc_' > bdry.f:(.text+0x309f): undefined reference to `userbc_' > bdry.f:(.text+0x31d9): undefined reference to `userbc_' > obj/bdry.o:bdry.f:(.text+0x3352): more undefined references to `userbc_' > follow > obj/conduct.o: In function `nekuq_': > conduct.f:(.text+0xdcf): undefined reference to `userq_' > obj/ic.o: In function `nekuic_': > ic.f:(.text+0x6a6): undefined reference to `useric_' > ic.f:(.text+0x980): undefined reference to `useric_' > ic.f:(.text+0xad0): undefined reference to `useric_' > obj/ssolv.o: In function `gostep_': > ssolv.f:(.text+0x1954): undefined reference to `userchk_' > obj/ssolv.o: In function `go1step_': > ssolv.f:(.text+0x2424): undefined reference to `userchk_' > obj/subs1.o: In function `nekuvp_': > subs1.f:(.text+0x90c): undefined reference to `uservp_' > collect2: error: ld returned 1 exit status > make: *** [nek5000] Error 1 > > Attached the .usr and .box files which I used. What about the turBox.f > file ? > All the best, > Barak > > > > Quoting nek5000-users at lists.mcs.anl.gov > : > >> Hi Barak, >> >> Just take the box file from turbChannel >> and set nelx nely nelz to (say) -8 -8 -8 >> with periodic BCs P ,P ,P ,P ,P , >> >> Then, use a blank .usr file and set ffx fry ffz to be the >> formulas you have below in userf() in the .usr file. >> >> Finally, add the following to usrdat2() >> >> a=0 >> b=2*pi >> call rescale_x(xm1,a,b) >> call rescale_x(ym1,a,b) >> call rescale_x(zm1,a,b) >> >> which will put your box on [0,2pi]^3. >> >> Paul >> >> >> ----- Original Message ----- >> From: nek5000-users at lists.mcs.anl.gov >> >> To: nek5000-users at lists.mcs.anl.gov >> >> Sent: Sunday, December 15, 2013 4:14:22 PM >> Subject: [Nek5000-users] turbulent 3d box >> >> Dear nek's, >> I would like to run the following problem: >> a 3D periodic box, small viscosity and the following forcing: >> >> fx=cos(y)+sin(z) >> fy=cos(z)+sin(x) >> fz=cos(x)+sin(y) >> >> Do you have a similar example? >> >> Many thanks, >> Barak >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl >> .govhttps://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> > > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -------------- next part -------------- A non-text attachment was scrubbed... Name: turbBox.tar.gz Type: application/x-tar Size: 50109 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Tue Dec 17 10:02:22 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 17 Dec 2013 11:02:22 -0500 Subject: [Nek5000-users] problem with interpolation with hpst.in Message-ID: Hi Josh, I attached hpts.in and .usr file which I use them for modified stenosis example. But this is such a weird problem in some case I can not do interpolation for certain number of points and it just gives me multiplication of number of points which in this example is 107. Is that anything wrong with interpolation points, does repeating the number in hpts.in make problem? (sorry about last mistake for sending mail! :) ) Thanks, Ami -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: hpts.in Type: application/octet-stream Size: 4514 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: stenosis.usr Type: application/octet-stream Size: 4199 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Tue Dec 17 19:29:08 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 18 Dec 2013 01:29:08 +0000 Subject: [Nek5000-users] turbulent 3d box In-Reply-To: References: , Message-ID: Hi Barak, I added a 3d periodic box under "3dbox" in the examples directory. Paul Dear nek's, I would like to run the following problem: a 3D periodic box, small viscosity and the following forcing: fx=cos(y)+sin(z) fy=cos(z)+sin(x) fz=cos(x)+sin(y) Do you have a similar example? Many thanks, Barak _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Wed Dec 18 07:52:21 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 18 Dec 2013 07:52:21 -0600 Subject: [Nek5000-users] problem with interpolation with hpst.in In-Reply-To: References: Message-ID: Ami, Nothing jumps out at me in your hpts.in or .usr file that should cause a problem. I might suggest doing something extremely simple, like setting up a simple box case and interpolate a few points that are inside the box to see if that works. Perhaps something that is machine specific is going on? Josh On Tue, Dec 17, 2013 at 10:02 AM, wrote: > Hi Josh, > > I attached hpts.in and .usr file which I use them for modified stenosis > example. But this is such a weird problem in some case I can not do > interpolation for certain number of points and it just gives me > multiplication of number of points which in this example is 107. > Is that anything wrong with interpolation points, does repeating the > number in hpts.in make problem? > > (sorry about last mistake for sending mail! :) ) > Thanks, > Ami > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -- Josh Camp "All that is necessary for the triumph of evil is that good men do nothing" -- Edmund Burke -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Dec 18 12:47:29 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 18 Dec 2013 13:47:29 -0500 Subject: [Nek5000-users] multiple grids Message-ID: Hello Neks I was wondering if we could have two separate grids in nek, a finer grid for temp in energy equation and a coarser grid for velocity (mass and momentum). Is this possible in nek? Regards, Hesam -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Dec 18 18:13:07 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 19 Dec 2013 02:13:07 +0200 Subject: [Nek5000-users] turbulent 3d box In-Reply-To: References: , Message-ID: Dear Paul, Thanks for the example. However, it runs but something seems to be wrong: the value of the velocity magnitude is too high to my experience. (it should be about |f| where f is the forcing (the correct max value is sqrt(3)). Two questions: 1. In b3d.rea the parameter p2 (viscos) is 10935. Is't too high? I used values such as 1/12 and smaller ones. 2. in b3d.f there is a routine userbc(..) where the parameter ux=uy=uz=0. does it mean that the velocity on the boundaries is set to zero? This is not the case which I solved (in previous DNS) and also it conflicts with the forcing. I think that this condition should be removed. Thanks very much for your help. Barak On 12/18/2013 03:29 AM, nek5000-users at lists.mcs.anl.gov wrote: > > Hi Barak, > > I added a 3d periodic box under "3dbox" in the examples > directory. > > Paul > > > Dear nek's, > I would like to run the following problem: > a 3D periodic box, small viscosity and the following forcing: > > fx=cos(y)+sin(z) > fy=cos(z)+sin(x) > fz=cos(x)+sin(y) > > Do you have a similar example? > > Many thanks, > Barak > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Fri Dec 20 03:58:35 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 20 Dec 2013 10:58:35 +0100 Subject: [Nek5000-users] fld output Message-ID: Hi Paul, Thank you very much for your detailed answer. It was of great help. I have managed to extract the data I wanted in a required format for a multi-processor case but with no MPIIO for now. I will continue to work through the usrchk() subroutine. Thank you once again, Best regards, JP -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sat Dec 21 17:24:53 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 22 Dec 2013 01:24:53 +0200 Subject: [Nek5000-users] turbulent 3d box In-Reply-To: References: , Message-ID: Hi Paul, Regarding the 3dbox: The forcing which I propose is known as the ABC flow (Arnold-Beltrami-Childress) and has steady solutions (in the form of ABC flow) with Re=1/nu (nu the viscosity) Re=<12 (in periodic box). The forcing should be in the form: f=Re*ABC in order to balance the dissipation term. This settings can serve as a benchmark for pure hydro/mhd problems. I tried to fix the example which you have sent me, but I don't succeed retreiving the expected values. I attach the relevant files( tarball file). Best regards, Barak On 12/18/2013 03:29 AM, nek5000-users at lists.mcs.anl.gov wrote: > > Hi Barak, > > I added a 3d periodic box under "3dbox" in the examples > directory. > > Paul > > > Dear nek's, > I would like to run the following problem: > a 3D periodic box, small viscosity and the following forcing: > > fx=cos(y)+sin(z) > fy=cos(z)+sin(x) > fz=cos(x)+sin(y) > > Do you have a similar example? > > Many thanks, > Barak > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -------------- next part -------------- A non-text attachment was scrubbed... Name: b3d.tar.gz Type: application/x-tar Size: 28509 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Sat Dec 21 17:54:22 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 21 Dec 2013 23:54:22 +0000 Subject: [Nek5000-users] turbulent 3d box In-Reply-To: References: , , Message-ID: Hi Barak, Thanks for the note about the ABC flow -- that's very useful. What is your target viscosity? If you want it to be 0.1, then you would set param 2 in the .rea file to be 0.1. Setting param 2 = -0.1 would imply that Re=0.1 or equivalently nu=10. Does this resolve the issue for you? Once it's working we could add it as a documented example in the example suite. Thanks! Paul ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Saturday, December 21, 2013 5:24 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] turbulent 3d box Hi Paul, Regarding the 3dbox: The forcing which I propose is known as the ABC flow (Arnold-Beltrami-Childress) and has steady solutions (in the form of ABC flow) with Re=1/nu (nu the viscosity) Re=<12 (in periodic box). The forcing should be in the form: f=Re*ABC in order to balance the dissipation term. This settings can serve as a benchmark for pure hydro/mhd problems. I tried to fix the example which you have sent me, but I don't succeed retreiving the expected values. I attach the relevant files( tarball file). Best regards, Barak On 12/18/2013 03:29 AM, nek5000-users at lists.mcs.anl.gov wrote: > > Hi Barak, > > I added a 3d periodic box under "3dbox" in the examples > directory. > > Paul > > > Dear nek's, > I would like to run the following problem: > a 3D periodic box, small viscosity and the following forcing: > > fx=cos(y)+sin(z) > fy=cos(z)+sin(x) > fz=cos(x)+sin(y) > > Do you have a similar example? > > Many thanks, > Barak > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Sun Dec 22 07:53:53 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 22 Dec 2013 15:53:53 +0200 Subject: [Nek5000-users] turbulent 3d box In-Reply-To: References: , , Message-ID: Hi Paul, It seems that something does not work, comparing my simulations using a standard spectral code (pseudo-spectral). For nu=0.1, I used 16 points for each space direction. Now for this case, the nonlinear terms vanish (just cancel each other) and the solution is just the ABC flow if you set it as initial condition. Then since the forcing is f=nu*ABC the dissipation term (Laplacian) dissipation=-nu*ABC and therefore the initial value (ABC) remains as it is. If we decrease the viscosity above the critical value of 1/12 (if I remember correctly) there is a bifurcation (Hopf...) and we obtain a new periodic solution (in time), where the ABC modes are dominating combined with some high wave numbers that are oscillating. From my first tests using NEK, I find that the velocity field (for nu>1/12) does not agree with the above characteristics. For example, the max magnitude of the velocity field should be for the ABC flow sqrt(3), whereas here I get a value close to 2.5. Do you have any idea what's wrong? If you wish to read some literature about the ABC flow as a forcing for Navier Stokes or as a prescribed velocity for generation of magnetic field (i.e., kinematic generation of magnetic field MHD): 1. D. Galloway and U. Frisch. A numerical investigation of magnetic field generation in a flow with chaotic streamlines. Geophysical & Astrophysical Fluid Dynamics, 29(1):13?18, 1984. 2. D. Galloway and U. Frisch. Dynamo action in a family of flows with chaotic streamlines. Geophysical & Astrophysical Fluid Dynamics, 36(1):53?83, 1986. 3. Podvigina, Pouquet, On the non-linear stability of the 1:1:1 ABC flow, Phys. D, Vol. 75, 4, 1994. With my best wishes, Barak ? Quoting nek5000-users at lists.mcs.anl.gov: > Hi Barak, > > Thanks for the note about the ABC flow -- that's very useful. > > What is your target viscosity? > If you want it to be 0.1, then you would set param 2 in the .rea > file to be 0.1. > Setting param 2 = -0.1 would imply that Re=0.1 or equivalently nu=10. > Does this resolve the issue for you? > > Once it's working we could add it as a documented example in the example > suite. > > Thanks! > > Paul > ________________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov > [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of > nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] > Sent: Saturday, December 21, 2013 5:24 PM > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] turbulent 3d box > > Hi Paul, > Regarding the 3dbox: > The forcing which I propose is known as the ABC flow > (Arnold-Beltrami-Childress) and has steady solutions (in the form of ABC > flow) with Re=1/nu (nu the viscosity) Re=<12 (in periodic box). > The forcing should be in the form: > f=Re*ABC in order to balance the dissipation term. > This settings can serve as a benchmark for pure hydro/mhd problems. > > I tried to fix the example which you have sent me, but I don't succeed > retreiving the expected values. > I attach the relevant files( tarball file). > Best regards, > Barak > > > > On 12/18/2013 03:29 AM, nek5000-users at lists.mcs.anl.gov wrote: > Hi Barak, >> >> I added a 3d periodic box under "3dbox" in the examples >> directory. >> >> Paul >> >> >> Dear nek's, >> I would like to run the following problem: >> a 3D periodic box, small viscosity and the following forcing: >> >> fx=cos(y)+sin(z) >> fy=cos(z)+sin(x) >> fz=cos(x)+sin(y) >> >> Do you have a similar example? >> >> Many thanks, >> Barak >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.govhttps://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sun Dec 22 09:05:40 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 22 Dec 2013 15:05:40 +0000 Subject: [Nek5000-users] turbulent 3d box In-Reply-To: References: , , , Message-ID: Hi Barak, If your initial condition is: ux=(cos(y)+sin(z)) uy=(cos(z)+sin(x)) uz=(cos(x)+sin(y)) and your domain is [0,2pi]^3, how is it possible that your velocity magnitude is less than 2? What is your measure of velocity magnitude? When I compute the L2 norm of this initial condition I'm seeing about 2.3+ Paul ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Sunday, December 22, 2013 7:53 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] turbulent 3d box Hi Paul, It seems that something does not work, comparing my simulations using a standard spectral code (pseudo-spectral). For nu=0.1, I used 16 points for each space direction. Now for this case, the nonlinear terms vanish (just cancel each other) and the solution is just the ABC flow if you set it as initial condition. Then since the forcing is f=nu*ABC the dissipation term (Laplacian) dissipation=-nu*ABC and therefore the initial value (ABC) remains as it is. If we decrease the viscosity above the critical value of 1/12 (if I remember correctly) there is a bifurcation (Hopf...) and we obtain a new periodic solution (in time), where the ABC modes are dominating combined with some high wave numbers that are oscillating. >From my first tests using NEK, I find that the velocity field (for nu>1/12) does not agree with the above characteristics. For example, the max magnitude of the velocity field should be for the ABC flow sqrt(3), whereas here I get a value close to 2.5. Do you have any idea what's wrong? If you wish to read some literature about the ABC flow as a forcing for Navier Stokes or as a prescribed velocity for generation of magnetic field (i.e., kinematic generation of magnetic field MHD): 1. D. Galloway and U. Frisch. A numerical investigation of magnetic field generation in a flow with chaotic streamlines. Geophysical & Astrophysical Fluid Dynamics, 29(1):13?18, 1984. 2. D. Galloway and U. Frisch. Dynamo action in a family of flows with chaotic streamlines. Geophysical & Astrophysical Fluid Dynamics, 36(1):53?83, 1986. 3. Podvigina, Pouquet, On the non-linear stability of the 1:1:1 ABC flow, Phys. D, Vol. 75, 4, 1994. With my best wishes, Barak Quoting nek5000-users at lists.mcs.anl.gov: Hi Barak, Thanks for the note about the ABC flow -- that's very useful. What is your target viscosity? If you want it to be 0.1, then you would set param 2 in the .rea file to be 0.1. Setting param 2 = -0.1 would imply that Re=0.1 or equivalently nu=10. Does this resolve the issue for you? Once it's working we could add it as a documented example in the example suite. Thanks! Paul ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Saturday, December 21, 2013 5:24 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] turbulent 3d box Hi Paul, Regarding the 3dbox: The forcing which I propose is known as the ABC flow (Arnold-Beltrami-Childress) and has steady solutions (in the form of ABC flow) with Re=1/nu (nu the viscosity) Re=<12 (in periodic box). The forcing should be in the form: f=Re*ABC in order to balance the dissipation term. This settings can serve as a benchmark for pure hydro/mhd problems. I tried to fix the example which you have sent me, but I don't succeed retreiving the expected values. I attach the relevant files( tarball file). Best regards, Barak On 12/18/2013 03:29 AM, nek5000-users at lists.mcs.anl.gov wrote: Hi Barak, I added a 3d periodic box under "3dbox" in the examples directory. Paul Dear nek's, I would like to run the following problem: a 3D periodic box, small viscosity and the following forcing: fx=cos(y)+sin(z) fy=cos(z)+sin(x) fz=cos(x)+sin(y) Do you have a similar example? Many thanks, Barak _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.govhttps://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sun Dec 22 11:04:29 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 22 Dec 2013 19:04:29 +0200 Subject: [Nek5000-users] turbulent 3d box In-Reply-To: References: , , , Message-ID: Hi Paul, My definition for velocity magnitude is: |v|=sqrt(ux^2+uy^2+uz^2) so if you see, there are two components in the form: cos^2(x)+sin^2(x) etc in each direction so in fact |v|=sqrt(3) for any x,y,z. Isn't correct? Barak On 12/22/2013 05:05 PM, nek5000-users at lists.mcs.anl.gov wrote: > > Hi Barak, > > If your initial condition is: > > ux=(cos(y)+sin(z)) > uy=(cos(z)+sin(x)) > uz=(cos(x)+sin(y)) > > and your domain is [0,2pi]^3, how is it possible that your velocity > magnitude > is less than 2? > > > What is your measure of velocity magnitude? When I compute the L2 > norm of this initial condition I'm seeing about 2.3+ > > Paul > > ------------------------------------------------------------------------ > *From:* nek5000-users-bounces at lists.mcs.anl.gov > [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of > nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] > *Sent:* Sunday, December 22, 2013 7:53 AM > *To:* nek5000-users at lists.mcs.anl.gov > *Subject:* Re: [Nek5000-users] turbulent 3d box > > Hi Paul, > It seems that something does not work, comparing my simulations using a > standard spectral code (pseudo-spectral). For nu=0.1, I used 16 points > for each space direction. Now for this case, the nonlinear terms vanish > (just cancel each other) and the solution is just the ABC flow if you > set it as initial condition. Then since the forcing is f=nu*ABC the > dissipation term (Laplacian) dissipation=-nu*ABC and therefore the > initial value (ABC) remains as it is. If we decrease the viscosity above > the critical value of 1/12 (if I remember correctly) there is a > bifurcation (Hopf...) and we obtain a new periodic solution (in time), > where the ABC modes are dominating combined with some high wave numbers > that are oscillating. > > >From my first tests using NEK, I find that the velocity field (for > nu>1/12) does not agree with the above characteristics. For example, the > max magnitude of the velocity field should be for the ABC flow sqrt(3), > whereas here I get a value close to 2.5. > > Do you have any idea what's wrong? > If you wish to read some literature about the ABC flow as a forcing for > Navier Stokes or as a prescribed velocity for generation of magnetic > field (i.e., kinematic generation of magnetic field MHD): > > 1. D. Galloway and U. Frisch. A numerical investigation of magnetic > field generation in a flow with chaotic streamlines. Geophysical & > Astrophysical Fluid Dynamics, 29(1):13?18, 1984. > > 2. D. Galloway and U. Frisch. Dynamo action in a family of flows with > chaotic streamlines. > Geophysical & Astrophysical Fluid Dynamics, 36(1):53?83, 1986. > > 3. Podvigina, Pouquet, On the non-linear stability of the 1:1:1 ABC flow, > Phys. D, Vol. 75, 4, 1994. > > > With my best wishes, > Barak > > > Quoting nek5000-users at lists.mcs.anl.gov > : > >> Hi Barak, >> >> Thanks for the note about the ABC flow -- that's very useful. >> >> What is your target viscosity? >> If you want it to be 0.1, then you would set param 2 in the .rea file >> to be 0.1. >> Setting param 2 = -0.1 would imply that Re=0.1 or equivalently nu=10. >> Does this resolve the issue for you? >> >> Once it's working we could add it as a documented example in the example >> suite. >> >> Thanks! >> >> Paul >> ________________________________________ >> From: nek5000-users-bounces at lists.mcs.anl.gov >> >> [nek5000-users-bounces at lists.mcs.anl.gov >> ] on behalf of >> nek5000-users at lists.mcs.anl.gov >> >> [nek5000-users at lists.mcs.anl.gov ] >> Sent: Saturday, December 21, 2013 5:24 PM >> To: nek5000-users at lists.mcs.anl.gov >> >> Subject: Re: [Nek5000-users] turbulent 3d box >> >> Hi Paul, >> Regarding the 3dbox: >> The forcing which I propose is known as the ABC flow >> (Arnold-Beltrami-Childress) and has steady solutions (in the form of ABC >> flow) with Re=1/nu (nu the viscosity) Re=<12 (in periodic box). >> The forcing should be in the form: >> f=Re*ABC in order to balance the dissipation term. >> This settings can serve as a benchmark for pure hydro/mhd problems. >> >> I tried to fix the example which you have sent me, but I don't succeed >> retreiving the expected values. >> I attach the relevant files( tarball file). >> Best regards, >> Barak >> >> >> >> On 12/18/2013 03:29 AM, nek5000-users at lists.mcs.anl.gov >> wrote: >> >>> Hi Barak, >>> >>> I added a 3d periodic box under "3dbox" in the examples >>> directory. >>> >>> Paul >>> >>> >>> Dear nek's, >>> I would like to run the following problem: >>> a 3D periodic box, small viscosity and the following forcing: >>> >>> fx=cos(y)+sin(z) >>> fy=cos(z)+sin(x) >>> fz=cos(x)+sin(y) >>> >>> Do you have a similar example? >>> >>> Many thanks, >>> Barak >>> >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl >> .govhttps://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > > > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Sun Dec 22 14:24:42 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 22 Dec 2013 20:24:42 +0000 Subject: [Nek5000-users] turbulent 3d box In-Reply-To: References: , , , , Message-ID: Hi Barak, When I compute the L2 norm of the function, given as: v2 = [ sum_i vx_i b_i vx_i + vy_i b_i vy_i + vz_i b_i vz_i / sum_i b_i ]^(1/2) it comes out to ~ 2.23 Note that there are some places where ux==2, uy==0, uz==1, which would give an L2 norm of sqrt (2*2 + 0*0 + 1*1) = sqrt(5) > sqrt(3) ? Paul ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Sunday, December 22, 2013 11:04 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] turbulent 3d box Hi Paul, My definition for velocity magnitude is: |v|=sqrt(ux^2+uy^2+uz^2) so if you see, there are two components in the form: cos^2(x)+sin^2(x) etc in each direction so in fact |v|=sqrt(3) for any x,y,z. Isn't correct? Barak On 12/22/2013 05:05 PM, nek5000-users at lists.mcs.anl.gov wrote: > > Hi Barak, > > If your initial condition is: > > ux=(cos(y)+sin(z)) > uy=(cos(z)+sin(x)) > uz=(cos(x)+sin(y)) > > and your domain is [0,2pi]^3, how is it possible that your velocity > magnitude > is less than 2? > > > What is your measure of velocity magnitude? When I compute the L2 > norm of this initial condition I'm seeing about 2.3+ > > Paul > > ------------------------------------------------------------------------ > *From:* nek5000-users-bounces at lists.mcs.anl.gov > [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of > nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] > *Sent:* Sunday, December 22, 2013 7:53 AM > *To:* nek5000-users at lists.mcs.anl.gov > *Subject:* Re: [Nek5000-users] turbulent 3d box > > Hi Paul, > It seems that something does not work, comparing my simulations using a > standard spectral code (pseudo-spectral). For nu=0.1, I used 16 points > for each space direction. Now for this case, the nonlinear terms vanish > (just cancel each other) and the solution is just the ABC flow if you > set it as initial condition. Then since the forcing is f=nu*ABC the > dissipation term (Laplacian) dissipation=-nu*ABC and therefore the > initial value (ABC) remains as it is. If we decrease the viscosity above > the critical value of 1/12 (if I remember correctly) there is a > bifurcation (Hopf...) and we obtain a new periodic solution (in time), > where the ABC modes are dominating combined with some high wave numbers > that are oscillating. > > >From my first tests using NEK, I find that the velocity field (for > nu>1/12) does not agree with the above characteristics. For example, the > max magnitude of the velocity field should be for the ABC flow sqrt(3), > whereas here I get a value close to 2.5. > > Do you have any idea what's wrong? > If you wish to read some literature about the ABC flow as a forcing for > Navier Stokes or as a prescribed velocity for generation of magnetic > field (i.e., kinematic generation of magnetic field MHD): > > 1. D. Galloway and U. Frisch. A numerical investigation of magnetic > field generation in a flow with chaotic streamlines. Geophysical & > Astrophysical Fluid Dynamics, 29(1):13?18, 1984. > > 2. D. Galloway and U. Frisch. Dynamo action in a family of flows with > chaotic streamlines. > Geophysical & Astrophysical Fluid Dynamics, 36(1):53?83, 1986. > > 3. Podvigina, Pouquet, On the non-linear stability of the 1:1:1 ABC flow, > Phys. D, Vol. 75, 4, 1994. > > > With my best wishes, > Barak > > > Quoting nek5000-users at lists.mcs.anl.gov > : > >> Hi Barak, >> >> Thanks for the note about the ABC flow -- that's very useful. >> >> What is your target viscosity? >> If you want it to be 0.1, then you would set param 2 in the .rea file >> to be 0.1. >> Setting param 2 = -0.1 would imply that Re=0.1 or equivalently nu=10. >> Does this resolve the issue for you? >> >> Once it's working we could add it as a documented example in the example >> suite. >> >> Thanks! >> >> Paul >> ________________________________________ >> From: nek5000-users-bounces at lists.mcs.anl.gov >> >> [nek5000-users-bounces at lists.mcs.anl.gov >> ] on behalf of >> nek5000-users at lists.mcs.anl.gov >> >> [nek5000-users at lists.mcs.anl.gov ] >> Sent: Saturday, December 21, 2013 5:24 PM >> To: nek5000-users at lists.mcs.anl.gov >> >> Subject: Re: [Nek5000-users] turbulent 3d box >> >> Hi Paul, >> Regarding the 3dbox: >> The forcing which I propose is known as the ABC flow >> (Arnold-Beltrami-Childress) and has steady solutions (in the form of ABC >> flow) with Re=1/nu (nu the viscosity) Re=<12 (in periodic box). >> The forcing should be in the form: >> f=Re*ABC in order to balance the dissipation term. >> This settings can serve as a benchmark for pure hydro/mhd problems. >> >> I tried to fix the example which you have sent me, but I don't succeed >> retreiving the expected values. >> I attach the relevant files( tarball file). >> Best regards, >> Barak >> >> >> >> On 12/18/2013 03:29 AM, nek5000-users at lists.mcs.anl.gov >> wrote: >> >>> Hi Barak, >>> >>> I added a 3d periodic box under "3dbox" in the examples >>> directory. >>> >>> Paul >>> >>> >>> Dear nek's, >>> I would like to run the following problem: >>> a 3D periodic box, small viscosity and the following forcing: >>> >>> fx=cos(y)+sin(z) >>> fy=cos(z)+sin(x) >>> fz=cos(x)+sin(y) >>> >>> Do you have a similar example? >>> >>> Many thanks, >>> Barak >>> >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl >> .govhttps://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > > > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Sun Dec 22 14:59:38 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 22 Dec 2013 22:59:38 +0200 Subject: [Nek5000-users] turbulent 3d box In-Reply-To: References: , , , , Message-ID: Dear Paul, You're right.I check your calculations and they are correct!!!. A huge mistake of mine. Sorry for bothering you. In fact what I meant was the energy in the velocity field which is sqrt(3)/2=\int (ux^2+uy^2+uz^2)dxdydz So now I am going to recheck your code for nu<1/12 and see if indeed I obtain those periodic solutions. Did you see the papers? Another question, again with the interpolation: is it spectrally accurate? How I compute velocity field derivatives? such as vorticity, pressure, or strain field in a spectral accuracy? Furthermore: how in general one computes the energy spectrum of the velocity field, and the energy in a particular wavenumber ? (in the spectral methods it is quite straightforward). Many thanks, Barak On 12/22/2013 10:24 PM, nek5000-users at lists.mcs.anl.gov wrote: > > Hi Barak, > > When I compute the L2 norm of the function, given as: > > v2 = [ sum_i vx_i b_i vx_i + vy_i b_i vy_i + vz_i b_i vz_i / sum_i b_i ]^(1/2) > > it comes out to ~ 2.23 > > Note that there are some places where ux==2, uy==0, uz==1, > which would give an L2 norm of > > sqrt (2*2 + 0*0 + 1*1) = sqrt(5) > sqrt(3) > > ? > > Paul > > ________________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] > Sent: Sunday, December 22, 2013 11:04 AM > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] turbulent 3d box > > Hi Paul, > My definition for velocity magnitude is: > |v|=sqrt(ux^2+uy^2+uz^2) > so if you see, there are two components in the form: > cos^2(x)+sin^2(x) > etc in each direction > so in fact > |v|=sqrt(3) for any x,y,z. > Isn't correct? > Barak > > On 12/22/2013 05:05 PM, nek5000-users at lists.mcs.anl.gov wrote: >> >> Hi Barak, >> >> If your initial condition is: >> >> ux=(cos(y)+sin(z)) >> uy=(cos(z)+sin(x)) >> uz=(cos(x)+sin(y)) >> >> and your domain is [0,2pi]^3, how is it possible that your velocity >> magnitude >> is less than 2? >> >> >> What is your measure of velocity magnitude? When I compute the L2 >> norm of this initial condition I'm seeing about 2.3+ >> >> Paul >> >> ------------------------------------------------------------------------ >> *From:* nek5000-users-bounces at lists.mcs.anl.gov >> [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of >> nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] >> *Sent:* Sunday, December 22, 2013 7:53 AM >> *To:* nek5000-users at lists.mcs.anl.gov >> *Subject:* Re: [Nek5000-users] turbulent 3d box >> >> Hi Paul, >> It seems that something does not work, comparing my simulations using a >> standard spectral code (pseudo-spectral). For nu=0.1, I used 16 points >> for each space direction. Now for this case, the nonlinear terms vanish >> (just cancel each other) and the solution is just the ABC flow if you >> set it as initial condition. Then since the forcing is f=nu*ABC the >> dissipation term (Laplacian) dissipation=-nu*ABC and therefore the >> initial value (ABC) remains as it is. If we decrease the viscosity above >> the critical value of 1/12 (if I remember correctly) there is a >> bifurcation (Hopf...) and we obtain a new periodic solution (in time), >> where the ABC modes are dominating combined with some high wave numbers >> that are oscillating. >> >> >From my first tests using NEK, I find that the velocity field (for >> nu>1/12) does not agree with the above characteristics. For example, the >> max magnitude of the velocity field should be for the ABC flow sqrt(3), >> whereas here I get a value close to 2.5. >> >> Do you have any idea what's wrong? >> If you wish to read some literature about the ABC flow as a forcing for >> Navier Stokes or as a prescribed velocity for generation of magnetic >> field (i.e., kinematic generation of magnetic field MHD): >> >> 1. D. Galloway and U. Frisch. A numerical investigation of magnetic >> field generation in a flow with chaotic streamlines. Geophysical & >> Astrophysical Fluid Dynamics, 29(1):13?18, 1984. >> >> 2. D. Galloway and U. Frisch. Dynamo action in a family of flows with >> chaotic streamlines. >> Geophysical & Astrophysical Fluid Dynamics, 36(1):53?83, 1986. >> >> 3. Podvigina, Pouquet, On the non-linear stability of the 1:1:1 ABC flow, >> Phys. D, Vol. 75, 4, 1994. >> >> >> With my best wishes, >> Barak >> >> >> Quoting nek5000-users at lists.mcs.anl.gov >> : >> >>> Hi Barak, >>> >>> Thanks for the note about the ABC flow -- that's very useful. >>> >>> What is your target viscosity? >>> If you want it to be 0.1, then you would set param 2 in the .rea file >>> to be 0.1. >>> Setting param 2 = -0.1 would imply that Re=0.1 or equivalently nu=10. >>> Does this resolve the issue for you? >>> >>> Once it's working we could add it as a documented example in the example >>> suite. >>> >>> Thanks! >>> >>> Paul >>> ________________________________________ >>> From: nek5000-users-bounces at lists.mcs.anl.gov >>> >>> [nek5000-users-bounces at lists.mcs.anl.gov >>> ] on behalf of >>> nek5000-users at lists.mcs.anl.gov >>> >>> [nek5000-users at lists.mcs.anl.gov ] >>> Sent: Saturday, December 21, 2013 5:24 PM >>> To: nek5000-users at lists.mcs.anl.gov >>> >>> Subject: Re: [Nek5000-users] turbulent 3d box >>> >>> Hi Paul, >>> Regarding the 3dbox: >>> The forcing which I propose is known as the ABC flow >>> (Arnold-Beltrami-Childress) and has steady solutions (in the form of ABC >>> flow) with Re=1/nu (nu the viscosity) Re=<12 (in periodic box). >>> The forcing should be in the form: >>> f=Re*ABC in order to balance the dissipation term. >>> This settings can serve as a benchmark for pure hydro/mhd problems. >>> >>> I tried to fix the example which you have sent me, but I don't succeed >>> retreiving the expected values. >>> I attach the relevant files( tarball file). >>> Best regards, >>> Barak >>> >>> >>> >>> On 12/18/2013 03:29 AM, nek5000-users at lists.mcs.anl.gov >>> wrote: >>> >>>> Hi Barak, >>>> >>>> I added a 3d periodic box under "3dbox" in the examples >>>> directory. >>>> >>>> Paul >>>> >>>> >>>> Dear nek's, >>>> I would like to run the following problem: >>>> a 3D periodic box, small viscosity and the following forcing: >>>> >>>> fx=cos(y)+sin(z) >>>> fy=cos(z)+sin(x) >>>> fz=cos(x)+sin(y) >>>> >>>> Do you have a similar example? >>>> >>>> Many thanks, >>>> Barak >>>> >>>> >>>> _______________________________________________ >>>> Nek5000-users mailing list >>>> Nek5000-users at lists.mcs.anl.gov >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>> _______________________________________________ >>>> Nek5000-users mailing list >>>> Nek5000-users at lists.mcs.anl.gov >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl >>> .govhttps://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >> >> >> >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Sun Dec 22 15:05:25 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 22 Dec 2013 23:05:25 +0200 Subject: [Nek5000-users] turbulent 3d box In-Reply-To: References: , , , , Message-ID: Hi Paul, Before I run problems with smaller viscosity: how I increase the resolution? and remesh the box? Barak On 12/22/2013 10:24 PM, nek5000-users at lists.mcs.anl.gov wrote: > > Hi Barak, > > When I compute the L2 norm of the function, given as: > > v2 = [ sum_i vx_i b_i vx_i + vy_i b_i vy_i + vz_i b_i vz_i / sum_i b_i ]^(1/2) > > it comes out to ~ 2.23 > > Note that there are some places where ux==2, uy==0, uz==1, > which would give an L2 norm of > > sqrt (2*2 + 0*0 + 1*1) = sqrt(5) > sqrt(3) > > ? > > Paul > > ________________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] > Sent: Sunday, December 22, 2013 11:04 AM > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] turbulent 3d box > > Hi Paul, > My definition for velocity magnitude is: > |v|=sqrt(ux^2+uy^2+uz^2) > so if you see, there are two components in the form: > cos^2(x)+sin^2(x) > etc in each direction > so in fact > |v|=sqrt(3) for any x,y,z. > Isn't correct? > Barak > > On 12/22/2013 05:05 PM, nek5000-users at lists.mcs.anl.gov wrote: >> >> Hi Barak, >> >> If your initial condition is: >> >> ux=(cos(y)+sin(z)) >> uy=(cos(z)+sin(x)) >> uz=(cos(x)+sin(y)) >> >> and your domain is [0,2pi]^3, how is it possible that your velocity >> magnitude >> is less than 2? >> >> >> What is your measure of velocity magnitude? When I compute the L2 >> norm of this initial condition I'm seeing about 2.3+ >> >> Paul >> >> ------------------------------------------------------------------------ >> *From:* nek5000-users-bounces at lists.mcs.anl.gov >> [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of >> nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] >> *Sent:* Sunday, December 22, 2013 7:53 AM >> *To:* nek5000-users at lists.mcs.anl.gov >> *Subject:* Re: [Nek5000-users] turbulent 3d box >> >> Hi Paul, >> It seems that something does not work, comparing my simulations using a >> standard spectral code (pseudo-spectral). For nu=0.1, I used 16 points >> for each space direction. Now for this case, the nonlinear terms vanish >> (just cancel each other) and the solution is just the ABC flow if you >> set it as initial condition. Then since the forcing is f=nu*ABC the >> dissipation term (Laplacian) dissipation=-nu*ABC and therefore the >> initial value (ABC) remains as it is. If we decrease the viscosity above >> the critical value of 1/12 (if I remember correctly) there is a >> bifurcation (Hopf...) and we obtain a new periodic solution (in time), >> where the ABC modes are dominating combined with some high wave numbers >> that are oscillating. >> >> >From my first tests using NEK, I find that the velocity field (for >> nu>1/12) does not agree with the above characteristics. For example, the >> max magnitude of the velocity field should be for the ABC flow sqrt(3), >> whereas here I get a value close to 2.5. >> >> Do you have any idea what's wrong? >> If you wish to read some literature about the ABC flow as a forcing for >> Navier Stokes or as a prescribed velocity for generation of magnetic >> field (i.e., kinematic generation of magnetic field MHD): >> >> 1. D. Galloway and U. Frisch. A numerical investigation of magnetic >> field generation in a flow with chaotic streamlines. Geophysical & >> Astrophysical Fluid Dynamics, 29(1):13?18, 1984. >> >> 2. D. Galloway and U. Frisch. Dynamo action in a family of flows with >> chaotic streamlines. >> Geophysical & Astrophysical Fluid Dynamics, 36(1):53?83, 1986. >> >> 3. Podvigina, Pouquet, On the non-linear stability of the 1:1:1 ABC flow, >> Phys. D, Vol. 75, 4, 1994. >> >> >> With my best wishes, >> Barak >> >> >> Quoting nek5000-users at lists.mcs.anl.gov >> : >> >>> Hi Barak, >>> >>> Thanks for the note about the ABC flow -- that's very useful. >>> >>> What is your target viscosity? >>> If you want it to be 0.1, then you would set param 2 in the .rea file >>> to be 0.1. >>> Setting param 2 = -0.1 would imply that Re=0.1 or equivalently nu=10. >>> Does this resolve the issue for you? >>> >>> Once it's working we could add it as a documented example in the example >>> suite. >>> >>> Thanks! >>> >>> Paul >>> ________________________________________ >>> From: nek5000-users-bounces at lists.mcs.anl.gov >>> >>> [nek5000-users-bounces at lists.mcs.anl.gov >>> ] on behalf of >>> nek5000-users at lists.mcs.anl.gov >>> >>> [nek5000-users at lists.mcs.anl.gov ] >>> Sent: Saturday, December 21, 2013 5:24 PM >>> To: nek5000-users at lists.mcs.anl.gov >>> >>> Subject: Re: [Nek5000-users] turbulent 3d box >>> >>> Hi Paul, >>> Regarding the 3dbox: >>> The forcing which I propose is known as the ABC flow >>> (Arnold-Beltrami-Childress) and has steady solutions (in the form of ABC >>> flow) with Re=1/nu (nu the viscosity) Re=<12 (in periodic box). >>> The forcing should be in the form: >>> f=Re*ABC in order to balance the dissipation term. >>> This settings can serve as a benchmark for pure hydro/mhd problems. >>> >>> I tried to fix the example which you have sent me, but I don't succeed >>> retreiving the expected values. >>> I attach the relevant files( tarball file). >>> Best regards, >>> Barak >>> >>> >>> >>> On 12/18/2013 03:29 AM, nek5000-users at lists.mcs.anl.gov >>> wrote: >>> >>>> Hi Barak, >>>> >>>> I added a 3d periodic box under "3dbox" in the examples >>>> directory. >>>> >>>> Paul >>>> >>>> >>>> Dear nek's, >>>> I would like to run the following problem: >>>> a 3D periodic box, small viscosity and the following forcing: >>>> >>>> fx=cos(y)+sin(z) >>>> fy=cos(z)+sin(x) >>>> fz=cos(x)+sin(y) >>>> >>>> Do you have a similar example? >>>> >>>> Many thanks, >>>> Barak >>>> >>>> >>>> _______________________________________________ >>>> Nek5000-users mailing list >>>> Nek5000-users at lists.mcs.anl.gov >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>> _______________________________________________ >>>> Nek5000-users mailing list >>>> Nek5000-users at lists.mcs.anl.gov >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl >>> .govhttps://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >> >> >> >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Sun Dec 22 15:14:59 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 22 Dec 2013 21:14:59 +0000 Subject: [Nek5000-users] turbulent 3d box In-Reply-To: References: , , , , , Message-ID: Hi Barak, You can either increase lx1,ly1, lz1 in SIZE and re-make, or you can change nelx,nely,nelz in the .box file. Did you resolve the issue with the initial condition? Paul ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Sunday, December 22, 2013 3:05 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] turbulent 3d box Hi Paul, Before I run problems with smaller viscosity: how I increase the resolution? and remesh the box? Barak On 12/22/2013 10:24 PM, nek5000-users at lists.mcs.anl.gov wrote: > > Hi Barak, > > When I compute the L2 norm of the function, given as: > > v2 = [ sum_i vx_i b_i vx_i + vy_i b_i vy_i + vz_i b_i vz_i / sum_i b_i ]^(1/2) > > it comes out to ~ 2.23 > > Note that there are some places where ux==2, uy==0, uz==1, > which would give an L2 norm of > > sqrt (2*2 + 0*0 + 1*1) = sqrt(5) > sqrt(3) > > ? > > Paul > > ________________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] > Sent: Sunday, December 22, 2013 11:04 AM > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] turbulent 3d box > > Hi Paul, > My definition for velocity magnitude is: > |v|=sqrt(ux^2+uy^2+uz^2) > so if you see, there are two components in the form: > cos^2(x)+sin^2(x) > etc in each direction > so in fact > |v|=sqrt(3) for any x,y,z. > Isn't correct? > Barak > > On 12/22/2013 05:05 PM, nek5000-users at lists.mcs.anl.gov wrote: >> >> Hi Barak, >> >> If your initial condition is: >> >> ux=(cos(y)+sin(z)) >> uy=(cos(z)+sin(x)) >> uz=(cos(x)+sin(y)) >> >> and your domain is [0,2pi]^3, how is it possible that your velocity >> magnitude >> is less than 2? >> >> >> What is your measure of velocity magnitude? When I compute the L2 >> norm of this initial condition I'm seeing about 2.3+ >> >> Paul >> >> ------------------------------------------------------------------------ >> *From:* nek5000-users-bounces at lists.mcs.anl.gov >> [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of >> nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] >> *Sent:* Sunday, December 22, 2013 7:53 AM >> *To:* nek5000-users at lists.mcs.anl.gov >> *Subject:* Re: [Nek5000-users] turbulent 3d box >> >> Hi Paul, >> It seems that something does not work, comparing my simulations using a >> standard spectral code (pseudo-spectral). For nu=0.1, I used 16 points >> for each space direction. Now for this case, the nonlinear terms vanish >> (just cancel each other) and the solution is just the ABC flow if you >> set it as initial condition. Then since the forcing is f=nu*ABC the >> dissipation term (Laplacian) dissipation=-nu*ABC and therefore the >> initial value (ABC) remains as it is. If we decrease the viscosity above >> the critical value of 1/12 (if I remember correctly) there is a >> bifurcation (Hopf...) and we obtain a new periodic solution (in time), >> where the ABC modes are dominating combined with some high wave numbers >> that are oscillating. >> >> >From my first tests using NEK, I find that the velocity field (for >> nu>1/12) does not agree with the above characteristics. For example, the >> max magnitude of the velocity field should be for the ABC flow sqrt(3), >> whereas here I get a value close to 2.5. >> >> Do you have any idea what's wrong? >> If you wish to read some literature about the ABC flow as a forcing for >> Navier Stokes or as a prescribed velocity for generation of magnetic >> field (i.e., kinematic generation of magnetic field MHD): >> >> 1. D. Galloway and U. Frisch. A numerical investigation of magnetic >> field generation in a flow with chaotic streamlines. Geophysical & >> Astrophysical Fluid Dynamics, 29(1):13?18, 1984. >> >> 2. D. Galloway and U. Frisch. Dynamo action in a family of flows with >> chaotic streamlines. >> Geophysical & Astrophysical Fluid Dynamics, 36(1):53?83, 1986. >> >> 3. Podvigina, Pouquet, On the non-linear stability of the 1:1:1 ABC flow, >> Phys. D, Vol. 75, 4, 1994. >> >> >> With my best wishes, >> Barak >> >> >> Quoting nek5000-users at lists.mcs.anl.gov >> : >> >>> Hi Barak, >>> >>> Thanks for the note about the ABC flow -- that's very useful. >>> >>> What is your target viscosity? >>> If you want it to be 0.1, then you would set param 2 in the .rea file >>> to be 0.1. >>> Setting param 2 = -0.1 would imply that Re=0.1 or equivalently nu=10. >>> Does this resolve the issue for you? >>> >>> Once it's working we could add it as a documented example in the example >>> suite. >>> >>> Thanks! >>> >>> Paul >>> ________________________________________ >>> From: nek5000-users-bounces at lists.mcs.anl.gov >>> >>> [nek5000-users-bounces at lists.mcs.anl.gov >>> ] on behalf of >>> nek5000-users at lists.mcs.anl.gov >>> >>> [nek5000-users at lists.mcs.anl.gov ] >>> Sent: Saturday, December 21, 2013 5:24 PM >>> To: nek5000-users at lists.mcs.anl.gov >>> >>> Subject: Re: [Nek5000-users] turbulent 3d box >>> >>> Hi Paul, >>> Regarding the 3dbox: >>> The forcing which I propose is known as the ABC flow >>> (Arnold-Beltrami-Childress) and has steady solutions (in the form of ABC >>> flow) with Re=1/nu (nu the viscosity) Re=<12 (in periodic box). >>> The forcing should be in the form: >>> f=Re*ABC in order to balance the dissipation term. >>> This settings can serve as a benchmark for pure hydro/mhd problems. >>> >>> I tried to fix the example which you have sent me, but I don't succeed >>> retreiving the expected values. >>> I attach the relevant files( tarball file). >>> Best regards, >>> Barak >>> >>> >>> >>> On 12/18/2013 03:29 AM, nek5000-users at lists.mcs.anl.gov >>> wrote: >>> >>>> Hi Barak, >>>> >>>> I added a 3d periodic box under "3dbox" in the examples >>>> directory. >>>> >>>> Paul >>>> >>>> >>>> Dear nek's, >>>> I would like to run the following problem: >>>> a 3D periodic box, small viscosity and the following forcing: >>>> >>>> fx=cos(y)+sin(z) >>>> fy=cos(z)+sin(x) >>>> fz=cos(x)+sin(y) >>>> >>>> Do you have a similar example? >>>> >>>> Many thanks, >>>> Barak >>>> >>>> >>>> _______________________________________________ >>>> Nek5000-users mailing list >>>> Nek5000-users at lists.mcs.anl.gov >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>> _______________________________________________ >>>> Nek5000-users mailing list >>>> Nek5000-users at lists.mcs.anl.gov >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl >>> .govhttps://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >> >> >> >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Sun Dec 22 15:20:31 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 22 Dec 2013 23:20:31 +0200 Subject: [Nek5000-users] turbulent 3d box In-Reply-To: References: , , , , , Message-ID: Hi Paul, On 12/22/2013 11:14 PM, nek5000-users at lists.mcs.anl.gov wrote: > > Hi Barak, > > You can either increase lx1,ly1, lz1 in SIZE and re-make, or you > can change nelx,nely,nelz in the .box file. > Thanks. > Did you resolve the issue with the initial condition? > See my previous email. I have inside further questions. Best regards, Barak > Paul > ________________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] > Sent: Sunday, December 22, 2013 3:05 PM > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] turbulent 3d box > > Hi Paul, > Before I run problems with smaller viscosity: how I increase the > resolution? and remesh the box? > Barak > > On 12/22/2013 10:24 PM, nek5000-users at lists.mcs.anl.gov wrote: >> >> Hi Barak, >> >> When I compute the L2 norm of the function, given as: >> >> v2 = [ sum_i vx_i b_i vx_i + vy_i b_i vy_i + vz_i b_i vz_i / sum_i b_i ]^(1/2) >> >> it comes out to ~ 2.23 >> >> Note that there are some places where ux==2, uy==0, uz==1, >> which would give an L2 norm of >> >> sqrt (2*2 + 0*0 + 1*1) = sqrt(5) > sqrt(3) >> >> ? >> >> Paul >> >> ________________________________________ >> From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] >> Sent: Sunday, December 22, 2013 11:04 AM >> To: nek5000-users at lists.mcs.anl.gov >> Subject: Re: [Nek5000-users] turbulent 3d box >> >> Hi Paul, >> My definition for velocity magnitude is: >> |v|=sqrt(ux^2+uy^2+uz^2) >> so if you see, there are two components in the form: >> cos^2(x)+sin^2(x) >> etc in each direction >> so in fact >> |v|=sqrt(3) for any x,y,z. >> Isn't correct? >> Barak >> >> On 12/22/2013 05:05 PM, nek5000-users at lists.mcs.anl.gov wrote: >>> >>> Hi Barak, >>> >>> If your initial condition is: >>> >>> ux=(cos(y)+sin(z)) >>> uy=(cos(z)+sin(x)) >>> uz=(cos(x)+sin(y)) >>> >>> and your domain is [0,2pi]^3, how is it possible that your velocity >>> magnitude >>> is less than 2? >>> >>> >>> What is your measure of velocity magnitude? When I compute the L2 >>> norm of this initial condition I'm seeing about 2.3+ >>> >>> Paul >>> >>> ------------------------------------------------------------------------ >>> *From:* nek5000-users-bounces at lists.mcs.anl.gov >>> [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of >>> nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] >>> *Sent:* Sunday, December 22, 2013 7:53 AM >>> *To:* nek5000-users at lists.mcs.anl.gov >>> *Subject:* Re: [Nek5000-users] turbulent 3d box >>> >>> Hi Paul, >>> It seems that something does not work, comparing my simulations using a >>> standard spectral code (pseudo-spectral). For nu=0.1, I used 16 points >>> for each space direction. Now for this case, the nonlinear terms vanish >>> (just cancel each other) and the solution is just the ABC flow if you >>> set it as initial condition. Then since the forcing is f=nu*ABC the >>> dissipation term (Laplacian) dissipation=-nu*ABC and therefore the >>> initial value (ABC) remains as it is. If we decrease the viscosity above >>> the critical value of 1/12 (if I remember correctly) there is a >>> bifurcation (Hopf...) and we obtain a new periodic solution (in time), >>> where the ABC modes are dominating combined with some high wave numbers >>> that are oscillating. >>> >>> >From my first tests using NEK, I find that the velocity field (for >>> nu>1/12) does not agree with the above characteristics. For example, the >>> max magnitude of the velocity field should be for the ABC flow sqrt(3), >>> whereas here I get a value close to 2.5. >>> >>> Do you have any idea what's wrong? >>> If you wish to read some literature about the ABC flow as a forcing for >>> Navier Stokes or as a prescribed velocity for generation of magnetic >>> field (i.e., kinematic generation of magnetic field MHD): >>> >>> 1. D. Galloway and U. Frisch. A numerical investigation of magnetic >>> field generation in a flow with chaotic streamlines. Geophysical & >>> Astrophysical Fluid Dynamics, 29(1):13?18, 1984. >>> >>> 2. D. Galloway and U. Frisch. Dynamo action in a family of flows with >>> chaotic streamlines. >>> Geophysical & Astrophysical Fluid Dynamics, 36(1):53?83, 1986. >>> >>> 3. Podvigina, Pouquet, On the non-linear stability of the 1:1:1 ABC flow, >>> Phys. D, Vol. 75, 4, 1994. >>> >>> >>> With my best wishes, >>> Barak >>> >>> >>> Quoting nek5000-users at lists.mcs.anl.gov >>> : >>> >>>> Hi Barak, >>>> >>>> Thanks for the note about the ABC flow -- that's very useful. >>>> >>>> What is your target viscosity? >>>> If you want it to be 0.1, then you would set param 2 in the .rea file >>>> to be 0.1. >>>> Setting param 2 = -0.1 would imply that Re=0.1 or equivalently nu=10. >>>> Does this resolve the issue for you? >>>> >>>> Once it's working we could add it as a documented example in the example >>>> suite. >>>> >>>> Thanks! >>>> >>>> Paul >>>> ________________________________________ >>>> From: nek5000-users-bounces at lists.mcs.anl.gov >>>> >>>> [nek5000-users-bounces at lists.mcs.anl.gov >>>> ] on behalf of >>>> nek5000-users at lists.mcs.anl.gov >>>> >>>> [nek5000-users at lists.mcs.anl.gov ] >>>> Sent: Saturday, December 21, 2013 5:24 PM >>>> To: nek5000-users at lists.mcs.anl.gov >>>> >>>> Subject: Re: [Nek5000-users] turbulent 3d box >>>> >>>> Hi Paul, >>>> Regarding the 3dbox: >>>> The forcing which I propose is known as the ABC flow >>>> (Arnold-Beltrami-Childress) and has steady solutions (in the form of ABC >>>> flow) with Re=1/nu (nu the viscosity) Re=<12 (in periodic box). >>>> The forcing should be in the form: >>>> f=Re*ABC in order to balance the dissipation term. >>>> This settings can serve as a benchmark for pure hydro/mhd problems. >>>> >>>> I tried to fix the example which you have sent me, but I don't succeed >>>> retreiving the expected values. >>>> I attach the relevant files( tarball file). >>>> Best regards, >>>> Barak >>>> >>>> >>>> >>>> On 12/18/2013 03:29 AM, nek5000-users at lists.mcs.anl.gov >>>> wrote: >>>> >>>>> Hi Barak, >>>>> >>>>> I added a 3d periodic box under "3dbox" in the examples >>>>> directory. >>>>> >>>>> Paul >>>>> >>>>> >>>>> Dear nek's, >>>>> I would like to run the following problem: >>>>> a 3D periodic box, small viscosity and the following forcing: >>>>> >>>>> fx=cos(y)+sin(z) >>>>> fy=cos(z)+sin(x) >>>>> fz=cos(x)+sin(y) >>>>> >>>>> Do you have a similar example? >>>>> >>>>> Many thanks, >>>>> Barak >>>>> >>>>> >>>>> _______________________________________________ >>>>> Nek5000-users mailing list >>>>> Nek5000-users at lists.mcs.anl.gov >>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>>> _______________________________________________ >>>>> Nek5000-users mailing list >>>>> Nek5000-users at lists.mcs.anl.gov >>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>>> >>>> _______________________________________________ >>>> Nek5000-users mailing list >>>> Nek5000-users at lists.mcs.anl >>>> .govhttps://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Sun Dec 22 15:22:44 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 22 Dec 2013 21:22:44 +0000 Subject: [Nek5000-users] turbulent 3d box In-Reply-To: References: , , , , , Message-ID: Hi Barak, Derivatives are best computed using gradm1(). See earlier posts on this topic. Interpolation is spectrally accurate, but you can also just integrate your fields against cos(kx), sin(kx), etc. and compute energy at a particular wave number in the old-fashioned way. The advantage of this approach is that it is trivially parallel -- but it's not optimal for performance if you want the full spectrum. At present, we don't have a full set of tools for 3D Fourier analysis of SEM flows because such flows are not standard; normally this code is applied in unstructured geometries. I think if you review the users lists you might find some discussion of transformations in a single direction, and we certainly do have tools that you could adapt for such purposes. If I were doing it, that's the route I would follow --- i.e., I would transform in one direction to get planes of differing wave numbers on each processor, then locally transform in the other directions. I would also first interpolate onto a uniform mesh in each element --- (grep -i zuni *.f in the /nek directory will lead you to calls to implement such a transformation). Note that you can interpolate from GLL to uniform --- that direction is stable. You cannot, however, transform from uniform to GLL. Paul ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Sunday, December 22, 2013 2:59 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] turbulent 3d box Dear Paul, You're right.I check your calculations and they are correct!!!. A huge mistake of mine. Sorry for bothering you. In fact what I meant was the energy in the velocity field which is sqrt(3)/2=\int (ux^2+uy^2+uz^2)dxdydz So now I am going to recheck your code for nu<1/12 and see if indeed I obtain those periodic solutions. Did you see the papers? Another question, again with the interpolation: is it spectrally accurate? How I compute velocity field derivatives? such as vorticity, pressure, or strain field in a spectral accuracy? Furthermore: how in general one computes the energy spectrum of the velocity field, and the energy in a particular wavenumber ? (in the spectral methods it is quite straightforward). Many thanks, Barak On 12/22/2013 10:24 PM, nek5000-users at lists.mcs.anl.gov wrote: > > Hi Barak, > > When I compute the L2 norm of the function, given as: > > v2 = [ sum_i vx_i b_i vx_i + vy_i b_i vy_i + vz_i b_i vz_i / sum_i b_i ]^(1/2) > > it comes out to ~ 2.23 > > Note that there are some places where ux==2, uy==0, uz==1, > which would give an L2 norm of > > sqrt (2*2 + 0*0 + 1*1) = sqrt(5) > sqrt(3) > > ? > > Paul > > ________________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] > Sent: Sunday, December 22, 2013 11:04 AM > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] turbulent 3d box > > Hi Paul, > My definition for velocity magnitude is: > |v|=sqrt(ux^2+uy^2+uz^2) > so if you see, there are two components in the form: > cos^2(x)+sin^2(x) > etc in each direction > so in fact > |v|=sqrt(3) for any x,y,z. > Isn't correct? > Barak > > On 12/22/2013 05:05 PM, nek5000-users at lists.mcs.anl.gov wrote: >> >> Hi Barak, >> >> If your initial condition is: >> >> ux=(cos(y)+sin(z)) >> uy=(cos(z)+sin(x)) >> uz=(cos(x)+sin(y)) >> >> and your domain is [0,2pi]^3, how is it possible that your velocity >> magnitude >> is less than 2? >> >> >> What is your measure of velocity magnitude? When I compute the L2 >> norm of this initial condition I'm seeing about 2.3+ >> >> Paul >> >> ------------------------------------------------------------------------ >> *From:* nek5000-users-bounces at lists.mcs.anl.gov >> [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of >> nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] >> *Sent:* Sunday, December 22, 2013 7:53 AM >> *To:* nek5000-users at lists.mcs.anl.gov >> *Subject:* Re: [Nek5000-users] turbulent 3d box >> >> Hi Paul, >> It seems that something does not work, comparing my simulations using a >> standard spectral code (pseudo-spectral). For nu=0.1, I used 16 points >> for each space direction. Now for this case, the nonlinear terms vanish >> (just cancel each other) and the solution is just the ABC flow if you >> set it as initial condition. Then since the forcing is f=nu*ABC the >> dissipation term (Laplacian) dissipation=-nu*ABC and therefore the >> initial value (ABC) remains as it is. If we decrease the viscosity above >> the critical value of 1/12 (if I remember correctly) there is a >> bifurcation (Hopf...) and we obtain a new periodic solution (in time), >> where the ABC modes are dominating combined with some high wave numbers >> that are oscillating. >> >> >From my first tests using NEK, I find that the velocity field (for >> nu>1/12) does not agree with the above characteristics. For example, the >> max magnitude of the velocity field should be for the ABC flow sqrt(3), >> whereas here I get a value close to 2.5. >> >> Do you have any idea what's wrong? >> If you wish to read some literature about the ABC flow as a forcing for >> Navier Stokes or as a prescribed velocity for generation of magnetic >> field (i.e., kinematic generation of magnetic field MHD): >> >> 1. D. Galloway and U. Frisch. A numerical investigation of magnetic >> field generation in a flow with chaotic streamlines. Geophysical & >> Astrophysical Fluid Dynamics, 29(1):13?18, 1984. >> >> 2. D. Galloway and U. Frisch. Dynamo action in a family of flows with >> chaotic streamlines. >> Geophysical & Astrophysical Fluid Dynamics, 36(1):53?83, 1986. >> >> 3. Podvigina, Pouquet, On the non-linear stability of the 1:1:1 ABC flow, >> Phys. D, Vol. 75, 4, 1994. >> >> >> With my best wishes, >> Barak >> >> >> Quoting nek5000-users at lists.mcs.anl.gov >> : >> >>> Hi Barak, >>> >>> Thanks for the note about the ABC flow -- that's very useful. >>> >>> What is your target viscosity? >>> If you want it to be 0.1, then you would set param 2 in the .rea file >>> to be 0.1. >>> Setting param 2 = -0.1 would imply that Re=0.1 or equivalently nu=10. >>> Does this resolve the issue for you? >>> >>> Once it's working we could add it as a documented example in the example >>> suite. >>> >>> Thanks! >>> >>> Paul >>> ________________________________________ >>> From: nek5000-users-bounces at lists.mcs.anl.gov >>> >>> [nek5000-users-bounces at lists.mcs.anl.gov >>> ] on behalf of >>> nek5000-users at lists.mcs.anl.gov >>> >>> [nek5000-users at lists.mcs.anl.gov ] >>> Sent: Saturday, December 21, 2013 5:24 PM >>> To: nek5000-users at lists.mcs.anl.gov >>> >>> Subject: Re: [Nek5000-users] turbulent 3d box >>> >>> Hi Paul, >>> Regarding the 3dbox: >>> The forcing which I propose is known as the ABC flow >>> (Arnold-Beltrami-Childress) and has steady solutions (in the form of ABC >>> flow) with Re=1/nu (nu the viscosity) Re=<12 (in periodic box). >>> The forcing should be in the form: >>> f=Re*ABC in order to balance the dissipation term. >>> This settings can serve as a benchmark for pure hydro/mhd problems. >>> >>> I tried to fix the example which you have sent me, but I don't succeed >>> retreiving the expected values. >>> I attach the relevant files( tarball file). >>> Best regards, >>> Barak >>> >>> >>> >>> On 12/18/2013 03:29 AM, nek5000-users at lists.mcs.anl.gov >>> wrote: >>> >>>> Hi Barak, >>>> >>>> I added a 3d periodic box under "3dbox" in the examples >>>> directory. >>>> >>>> Paul >>>> >>>> >>>> Dear nek's, >>>> I would like to run the following problem: >>>> a 3D periodic box, small viscosity and the following forcing: >>>> >>>> fx=cos(y)+sin(z) >>>> fy=cos(z)+sin(x) >>>> fz=cos(x)+sin(y) >>>> >>>> Do you have a similar example? >>>> >>>> Many thanks, >>>> Barak >>>> >>>> >>>> _______________________________________________ >>>> Nek5000-users mailing list >>>> Nek5000-users at lists.mcs.anl.gov >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>> _______________________________________________ >>>> Nek5000-users mailing list >>>> Nek5000-users at lists.mcs.anl.gov >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl >>> .govhttps://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >> >> >> >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Sun Dec 22 15:46:31 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 22 Dec 2013 23:46:31 +0200 Subject: [Nek5000-users] turbulent 3d box In-Reply-To: References: , , , , , Message-ID: considering changing the box mesh: see the following attachment. Thanks, Barak On 12/22/2013 11:20 PM, nek5000-users at lists.mcs.anl.gov wrote: > > Hi Paul, > On 12/22/2013 11:14 PM, nek5000-users at lists.mcs.anl.gov wrote: >> >> Hi Barak, >> >> You can either increase lx1,ly1, lz1 in SIZE and re-make, or you >> can change nelx,nely,nelz in the .box file. >> > Thanks. >> Did you resolve the issue with the initial condition? >> > See my previous email. I have inside further questions. > Best regards, > Barak > > >> Paul >> ________________________________________ >> From: nek5000-users-bounces at lists.mcs.anl.gov >> [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of >> nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] >> Sent: Sunday, December 22, 2013 3:05 PM >> To: nek5000-users at lists.mcs.anl.gov >> Subject: Re: [Nek5000-users] turbulent 3d box >> >> Hi Paul, >> Before I run problems with smaller viscosity: how I increase the >> resolution? and remesh the box? >> Barak >> >> On 12/22/2013 10:24 PM, nek5000-users at lists.mcs.anl.gov wrote: >>> >>> Hi Barak, >>> >>> When I compute the L2 norm of the function, given as: >>> >>> v2 = [ sum_i vx_i b_i vx_i + vy_i b_i vy_i + vz_i b_i vz_i >>> / sum_i b_i ]^(1/2) >>> >>> it comes out to ~ 2.23 >>> >>> Note that there are some places where ux==2, uy==0, uz==1, >>> which would give an L2 norm of >>> >>> sqrt (2*2 + 0*0 + 1*1) = sqrt(5) > sqrt(3) >>> >>> ? >>> >>> Paul >>> >>> ________________________________________ >>> From: nek5000-users-bounces at lists.mcs.anl.gov >>> [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of >>> nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] >>> Sent: Sunday, December 22, 2013 11:04 AM >>> To: nek5000-users at lists.mcs.anl.gov >>> Subject: Re: [Nek5000-users] turbulent 3d box >>> >>> Hi Paul, >>> My definition for velocity magnitude is: >>> |v|=sqrt(ux^2+uy^2+uz^2) >>> so if you see, there are two components in the form: >>> cos^2(x)+sin^2(x) >>> etc in each direction >>> so in fact >>> |v|=sqrt(3) for any x,y,z. >>> Isn't correct? >>> Barak >>> >>> On 12/22/2013 05:05 PM, nek5000-users at lists.mcs.anl.gov wrote: >>>> >>>> Hi Barak, >>>> >>>> If your initial condition is: >>>> >>>> ux=(cos(y)+sin(z)) >>>> uy=(cos(z)+sin(x)) >>>> uz=(cos(x)+sin(y)) >>>> >>>> and your domain is [0,2pi]^3, how is it possible that your velocity >>>> magnitude >>>> is less than 2? >>>> >>>> >>>> What is your measure of velocity magnitude? When I compute the L2 >>>> norm of this initial condition I'm seeing about 2.3+ >>>> >>>> Paul >>>> >>>> ------------------------------------------------------------------------ >>>> >>>> *From:* nek5000-users-bounces at lists.mcs.anl.gov >>>> [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of >>>> nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] >>>> *Sent:* Sunday, December 22, 2013 7:53 AM >>>> *To:* nek5000-users at lists.mcs.anl.gov >>>> *Subject:* Re: [Nek5000-users] turbulent 3d box >>>> >>>> Hi Paul, >>>> It seems that something does not work, comparing my simulations using a >>>> standard spectral code (pseudo-spectral). For nu=0.1, I used 16 points >>>> for each space direction. Now for this case, the nonlinear terms vanish >>>> (just cancel each other) and the solution is just the ABC flow if you >>>> set it as initial condition. Then since the forcing is f=nu*ABC the >>>> dissipation term (Laplacian) dissipation=-nu*ABC and therefore the >>>> initial value (ABC) remains as it is. If we decrease the viscosity >>>> above >>>> the critical value of 1/12 (if I remember correctly) there is a >>>> bifurcation (Hopf...) and we obtain a new periodic solution (in time), >>>> where the ABC modes are dominating combined with some high wave numbers >>>> that are oscillating. >>>> >>>> >From my first tests using NEK, I find that the velocity field (for >>>> nu>1/12) does not agree with the above characteristics. For example, >>>> the >>>> max magnitude of the velocity field should be for the ABC flow sqrt(3), >>>> whereas here I get a value close to 2.5. >>>> >>>> Do you have any idea what's wrong? >>>> If you wish to read some literature about the ABC flow as a forcing for >>>> Navier Stokes or as a prescribed velocity for generation of magnetic >>>> field (i.e., kinematic generation of magnetic field MHD): >>>> >>>> 1. D. Galloway and U. Frisch. A numerical investigation of magnetic >>>> field generation in a flow with chaotic streamlines. Geophysical & >>>> Astrophysical Fluid Dynamics, 29(1):13?18, 1984. >>>> >>>> 2. D. Galloway and U. Frisch. Dynamo action in a family of flows with >>>> chaotic streamlines. >>>> Geophysical & Astrophysical Fluid Dynamics, 36(1):53?83, 1986. >>>> >>>> 3. Podvigina, Pouquet, On the non-linear stability of the 1:1:1 ABC >>>> flow, >>>> Phys. D, Vol. 75, 4, 1994. >>>> >>>> >>>> With my best wishes, >>>> Barak >>>> >>>> >>>> Quoting nek5000-users at lists.mcs.anl.gov >>>> : >>>> >>>>> Hi Barak, >>>>> >>>>> Thanks for the note about the ABC flow -- that's very useful. >>>>> >>>>> What is your target viscosity? >>>>> If you want it to be 0.1, then you would set param 2 in the .rea file >>>>> to be 0.1. >>>>> Setting param 2 = -0.1 would imply that Re=0.1 or equivalently nu=10. >>>>> Does this resolve the issue for you? >>>>> >>>>> Once it's working we could add it as a documented example in the >>>>> example >>>>> suite. >>>>> >>>>> Thanks! >>>>> >>>>> Paul >>>>> ________________________________________ >>>>> From: nek5000-users-bounces at lists.mcs.anl.gov >>>>> >>>>> [nek5000-users-bounces at lists.mcs.anl.gov >>>>> ] on behalf of >>>>> nek5000-users at lists.mcs.anl.gov >>>>> >>>>> [nek5000-users at lists.mcs.anl.gov >>>>> ] >>>>> Sent: Saturday, December 21, 2013 5:24 PM >>>>> To: nek5000-users at lists.mcs.anl.gov >>>>> >>>>> Subject: Re: [Nek5000-users] turbulent 3d box >>>>> >>>>> Hi Paul, >>>>> Regarding the 3dbox: >>>>> The forcing which I propose is known as the ABC flow >>>>> (Arnold-Beltrami-Childress) and has steady solutions (in the form >>>>> of ABC >>>>> flow) with Re=1/nu (nu the viscosity) Re=<12 (in periodic box). >>>>> The forcing should be in the form: >>>>> f=Re*ABC in order to balance the dissipation term. >>>>> This settings can serve as a benchmark for pure hydro/mhd problems. >>>>> >>>>> I tried to fix the example which you have sent me, but I don't succeed >>>>> retreiving the expected values. >>>>> I attach the relevant files( tarball file). >>>>> Best regards, >>>>> Barak >>>>> >>>>> >>>>> >>>>> On 12/18/2013 03:29 AM, nek5000-users at lists.mcs.anl.gov >>>>> wrote: >>>>> >>>>>> Hi Barak, >>>>>> >>>>>> I added a 3d periodic box under "3dbox" in the examples >>>>>> directory. >>>>>> >>>>>> Paul >>>>>> >>>>>> >>>>>> Dear nek's, >>>>>> I would like to run the following problem: >>>>>> a 3D periodic box, small viscosity and the following forcing: >>>>>> >>>>>> fx=cos(y)+sin(z) >>>>>> fy=cos(z)+sin(x) >>>>>> fz=cos(x)+sin(y) >>>>>> >>>>>> Do you have a similar example? >>>>>> >>>>>> Many thanks, >>>>>> Barak >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Nek5000-users mailing list >>>>>> Nek5000-users at lists.mcs.anl.gov >>>>>> >>>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>>>> _______________________________________________ >>>>>> Nek5000-users mailing list >>>>>> Nek5000-users at lists.mcs.anl.gov >>>>>> >>>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>>>> >>>>> _______________________________________________ >>>>> Nek5000-users mailing list >>>>> Nek5000-users at lists.mcs.anl >>>>> .govhttps://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>>> >>>>> >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Nek5000-users mailing list >>>> Nek5000-users at lists.mcs.anl.gov >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>> >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -------------- next part -------------- A non-text attachment was scrubbed... Name: b3d_new.tar.gz Type: application/x-tar Size: 3195 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Sun Dec 22 16:25:16 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 23 Dec 2013 00:25:16 +0200 Subject: [Nek5000-users] turbulent 3d box In-Reply-To: References: , , , , , Message-ID: It didn't work (I tried both options). Do you have working example? (see my previous email and my attachment). Barak On 12/22/2013 11:20 PM, nek5000-users at lists.mcs.anl.gov wrote: > > Hi Paul, > On 12/22/2013 11:14 PM, nek5000-users at lists.mcs.anl.gov wrote: >> >> Hi Barak, >> >> You can either increase lx1,ly1, lz1 in SIZE and re-make, or you >> can change nelx,nely,nelz in the .box file. >> > Thanks. >> Did you resolve the issue with the initial condition? >> > See my previous email. I have inside further questions. > Best regards, > Barak > > >> Paul >> ________________________________________ >> From: nek5000-users-bounces at lists.mcs.anl.gov >> [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of >> nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] >> Sent: Sunday, December 22, 2013 3:05 PM >> To: nek5000-users at lists.mcs.anl.gov >> Subject: Re: [Nek5000-users] turbulent 3d box >> >> Hi Paul, >> Before I run problems with smaller viscosity: how I increase the >> resolution? and remesh the box? >> Barak >> >> On 12/22/2013 10:24 PM, nek5000-users at lists.mcs.anl.gov wrote: >>> >>> Hi Barak, >>> >>> When I compute the L2 norm of the function, given as: >>> >>> v2 = [ sum_i vx_i b_i vx_i + vy_i b_i vy_i + vz_i b_i vz_i >>> / sum_i b_i ]^(1/2) >>> >>> it comes out to ~ 2.23 >>> >>> Note that there are some places where ux==2, uy==0, uz==1, >>> which would give an L2 norm of >>> >>> sqrt (2*2 + 0*0 + 1*1) = sqrt(5) > sqrt(3) >>> >>> ? >>> >>> Paul >>> >>> ________________________________________ >>> From: nek5000-users-bounces at lists.mcs.anl.gov >>> [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of >>> nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] >>> Sent: Sunday, December 22, 2013 11:04 AM >>> To: nek5000-users at lists.mcs.anl.gov >>> Subject: Re: [Nek5000-users] turbulent 3d box >>> >>> Hi Paul, >>> My definition for velocity magnitude is: >>> |v|=sqrt(ux^2+uy^2+uz^2) >>> so if you see, there are two components in the form: >>> cos^2(x)+sin^2(x) >>> etc in each direction >>> so in fact >>> |v|=sqrt(3) for any x,y,z. >>> Isn't correct? >>> Barak >>> >>> On 12/22/2013 05:05 PM, nek5000-users at lists.mcs.anl.gov wrote: >>>> >>>> Hi Barak, >>>> >>>> If your initial condition is: >>>> >>>> ux=(cos(y)+sin(z)) >>>> uy=(cos(z)+sin(x)) >>>> uz=(cos(x)+sin(y)) >>>> >>>> and your domain is [0,2pi]^3, how is it possible that your velocity >>>> magnitude >>>> is less than 2? >>>> >>>> >>>> What is your measure of velocity magnitude? When I compute the L2 >>>> norm of this initial condition I'm seeing about 2.3+ >>>> >>>> Paul >>>> >>>> ------------------------------------------------------------------------ >>>> >>>> *From:* nek5000-users-bounces at lists.mcs.anl.gov >>>> [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of >>>> nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] >>>> *Sent:* Sunday, December 22, 2013 7:53 AM >>>> *To:* nek5000-users at lists.mcs.anl.gov >>>> *Subject:* Re: [Nek5000-users] turbulent 3d box >>>> >>>> Hi Paul, >>>> It seems that something does not work, comparing my simulations using a >>>> standard spectral code (pseudo-spectral). For nu=0.1, I used 16 points >>>> for each space direction. Now for this case, the nonlinear terms vanish >>>> (just cancel each other) and the solution is just the ABC flow if you >>>> set it as initial condition. Then since the forcing is f=nu*ABC the >>>> dissipation term (Laplacian) dissipation=-nu*ABC and therefore the >>>> initial value (ABC) remains as it is. If we decrease the viscosity >>>> above >>>> the critical value of 1/12 (if I remember correctly) there is a >>>> bifurcation (Hopf...) and we obtain a new periodic solution (in time), >>>> where the ABC modes are dominating combined with some high wave numbers >>>> that are oscillating. >>>> >>>> >From my first tests using NEK, I find that the velocity field (for >>>> nu>1/12) does not agree with the above characteristics. For example, >>>> the >>>> max magnitude of the velocity field should be for the ABC flow sqrt(3), >>>> whereas here I get a value close to 2.5. >>>> >>>> Do you have any idea what's wrong? >>>> If you wish to read some literature about the ABC flow as a forcing for >>>> Navier Stokes or as a prescribed velocity for generation of magnetic >>>> field (i.e., kinematic generation of magnetic field MHD): >>>> >>>> 1. D. Galloway and U. Frisch. A numerical investigation of magnetic >>>> field generation in a flow with chaotic streamlines. Geophysical & >>>> Astrophysical Fluid Dynamics, 29(1):13?18, 1984. >>>> >>>> 2. D. Galloway and U. Frisch. Dynamo action in a family of flows with >>>> chaotic streamlines. >>>> Geophysical & Astrophysical Fluid Dynamics, 36(1):53?83, 1986. >>>> >>>> 3. Podvigina, Pouquet, On the non-linear stability of the 1:1:1 ABC >>>> flow, >>>> Phys. D, Vol. 75, 4, 1994. >>>> >>>> >>>> With my best wishes, >>>> Barak >>>> >>>> >>>> Quoting nek5000-users at lists.mcs.anl.gov >>>> : >>>> >>>>> Hi Barak, >>>>> >>>>> Thanks for the note about the ABC flow -- that's very useful. >>>>> >>>>> What is your target viscosity? >>>>> If you want it to be 0.1, then you would set param 2 in the .rea file >>>>> to be 0.1. >>>>> Setting param 2 = -0.1 would imply that Re=0.1 or equivalently nu=10. >>>>> Does this resolve the issue for you? >>>>> >>>>> Once it's working we could add it as a documented example in the >>>>> example >>>>> suite. >>>>> >>>>> Thanks! >>>>> >>>>> Paul >>>>> ________________________________________ >>>>> From: nek5000-users-bounces at lists.mcs.anl.gov >>>>> >>>>> [nek5000-users-bounces at lists.mcs.anl.gov >>>>> ] on behalf of >>>>> nek5000-users at lists.mcs.anl.gov >>>>> >>>>> [nek5000-users at lists.mcs.anl.gov >>>>> ] >>>>> Sent: Saturday, December 21, 2013 5:24 PM >>>>> To: nek5000-users at lists.mcs.anl.gov >>>>> >>>>> Subject: Re: [Nek5000-users] turbulent 3d box >>>>> >>>>> Hi Paul, >>>>> Regarding the 3dbox: >>>>> The forcing which I propose is known as the ABC flow >>>>> (Arnold-Beltrami-Childress) and has steady solutions (in the form >>>>> of ABC >>>>> flow) with Re=1/nu (nu the viscosity) Re=<12 (in periodic box). >>>>> The forcing should be in the form: >>>>> f=Re*ABC in order to balance the dissipation term. >>>>> This settings can serve as a benchmark for pure hydro/mhd problems. >>>>> >>>>> I tried to fix the example which you have sent me, but I don't succeed >>>>> retreiving the expected values. >>>>> I attach the relevant files( tarball file). >>>>> Best regards, >>>>> Barak >>>>> >>>>> >>>>> >>>>> On 12/18/2013 03:29 AM, nek5000-users at lists.mcs.anl.gov >>>>> wrote: >>>>> >>>>>> Hi Barak, >>>>>> >>>>>> I added a 3d periodic box under "3dbox" in the examples >>>>>> directory. >>>>>> >>>>>> Paul >>>>>> >>>>>> >>>>>> Dear nek's, >>>>>> I would like to run the following problem: >>>>>> a 3D periodic box, small viscosity and the following forcing: >>>>>> >>>>>> fx=cos(y)+sin(z) >>>>>> fy=cos(z)+sin(x) >>>>>> fz=cos(x)+sin(y) >>>>>> >>>>>> Do you have a similar example? >>>>>> >>>>>> Many thanks, >>>>>> Barak >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Nek5000-users mailing list >>>>>> Nek5000-users at lists.mcs.anl.gov >>>>>> >>>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>>>> _______________________________________________ >>>>>> Nek5000-users mailing list >>>>>> Nek5000-users at lists.mcs.anl.gov >>>>>> >>>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>>>> >>>>> _______________________________________________ >>>>> Nek5000-users mailing list >>>>> Nek5000-users at lists.mcs.anl >>>>> .govhttps://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>>> >>>>> >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Nek5000-users mailing list >>>> Nek5000-users at lists.mcs.anl.gov >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>> >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >