June 2018 - Nektar-users - imperial.ac.uk

Regarding CSV to FLD convertor
by Abhishek Kumar 11 Jun '18

11 Jun '18

Dear friends, I am trying to modify the output of Nektar++ data. For that, I convert the data to csv and done the process in python. Now, I want to convert the csv data to fld to run on Nektar++. Is there any way to convert csv file to fld file? With regards Abhishek Kumar --------------------------------------------------------------------------------------- Abhishek Kumar Research Associate Applied Mathematics Research Centre Coventry University, Coventry CV1 5FB The United Kingdom Email # ac7600(a)coventry.ac.uk, abhishek.kir(a)gmail.com ---------------------------------------------------------------------------------------

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Failed to build thirdparty PETSc and Arpack
by #SHI ZIJI# 07 Jun '18

07 Jun '18

Dear all, I am trying to build Nektar++4.4.1 with third party PETSc and Arpack. The third party version of PETSc compiles, but it failed all of the tests. I executed the test command and it returned seg fault (seg fault for first 4 tests and exception for the rest). However, if I removed NEKTAR_USE_PETSC and THIRDPARTY_BUILD_PETSC, the tests can be passed. The command I used looks like the following: CC=mpiicc CXX=mpiicpc FC=mpiifort cmake\ -DNEKTAR_USE_MKL=ON \ -DNEKTAR_USE_PETSC=ON \ -DNEKTAR_USE_MPI=ON \ -DTHIRDPARTY_BUILD_PETSC=ON .. The test log is attached in this email. Meanwhile, may I know if Arpack can be supported with third party build? The cmake/ThirdPartyArpack.cmake is more like a FindArpack.cmake script. Many thanks in advance! Best Regards, Ziji

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boundary condintion file for CompressibleFlowSolver in neakar
by Chunhui Liu 06 Jun '18

06 Jun '18

Hi everyone, I am trying to use nektar++ for a simulation of convergence and divergence nozzle. https://www.grc.nasa.gov/www/wind/valid/cdv/cdv01/cdv01.html subsonic inlet and outlet case. From test case, my outlet bc was set as pressure out flow, followed the user guide. However my simulation always diverged. I don't know the reason. Is there anyone familar with boundary condition in nektar for a nozzle simulation? In addition, I noticed that in the source code CompressibleFlowSolver there are quite a lot boundary condition. However I don't know the syntax to write these boundary condition in .xml file. Thanks! <CONDITIONS> <PARAMETERS> TimeStep = 0.00001 NumSteps = 10 FinTime = TimeStep*NumSteps IO_CheckSteps = 1 IO_InfoSteps = 1 GasConstant = 287.058 Gamma = 1.4 pInf = 0.9617 rhoInf =0.000034471 uInf =46.77 vInf = 0.0 </PARAMETERS> <SOLVERINFO> </SOLVERINFO> <BOUNDARYREGIONS> C[2]  C[3]  C[4]  </BOUNDARYREGIONS> <BOUNDARYCONDITIONS> <REGION REF="0">  <D VAR="rho" VALUE="rhoInf" /> <D VAR="rhou" VALUE="rhoInf * uInf" /> <D VAR="rhov" VALUE="rhoInf * vInf" /> <D VAR="E" VALUE="pInf / (Gamma - 1) + 0.5 * rhoInf * (uInf * uInf + vInf * vInf)"/> </REGION> <REGION REF="1">  <D VAR="rho" USERDEFINEDTYPE="PressureOutflow" VALUE="0" /> <D VAR="rhou" USERDEFINEDTYPE="PressureOutflow" VALUE="0" /> <D VAR="rhov" USERDEFINEDTYPE="PressureOutflow" VALUE="0" /> <D VAR="E" USERDEFINEDTYPE="PressureOutflow" VALUE="0" /> </REGION> Chunhui Liu Mechanical and Mechatronics Engineering University of Waterloo

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Re: [Nektar-users] Compile the last version nektar++ shows link errors
by liuwenjie＠hit.edu.cn 06 Jun '18

06 Jun '18

Dear Dave Very thanks for your help! I tried it, but it still shows the same link errors. I guess the errors possible from "cxx11". All the best! Wenjie Liu > -----Original Messages----- > From: "David Moxey" <D.Moxey(a)exeter.ac.uk> > Sent Time: 2018-06-06 18:49:45 (Wednesday) > To: liuwenjie(a)hit.edu.cn > Cc: nektar-users(a)imperial.ac.uk > Subject: Re: [Nektar-users] Compile the last version nektar++ shows link errors > > Hi Wenjie, > > It looks like TinyXML might not have been installed correctly. One option might be for you to use the Debian package (libtinyxml-dev) and see if that is better? > > Cheers, > > Dave > > > On 6 Jun 2018, at 10:37, <liuwenjie(a)hit.edu.cn> <liuwenjie(a)hit.edu.cn> wrote: > > > > Dear all > > I compile the last version nektar++, used g++ 8.0.1 and cmake 3.11.2 in 64 ubuntu. > > I tried some suggestions. It still shows the following link errors. > > Can you given me some advice? Very thanks! > > > > > > Pde2016@ubuntu-1:~/libs/nektar++/build$ cmake -DCMAKE_INSTALL_PREFIX=/home/Pde2016/Bin/nektar-4.5.0 .. > > -- Found TinyXML: /usr/local/lib/libtinyxml.a > > -- Build Scotch: /home/Pde2016/libs/nektar++/build/ThirdParty/dist/lib/libscotch.a > > -- Found Zlib: /usr/lib/x86_64-linux-gnu/libz.so (version 1.2.8) > > -- Searching for Boost: > > -- -- Found Boost thread library: /usr/local/lib/libboost_thread.so > > -- -- Found Boost iostreams library: /usr/local/lib/libboost_iostreams.so > > -- -- Found Boost filesystem library: /usr/local/lib/libboost_filesystem.so > > -- -- Found Boost system library: /usr/local/lib/libboost_system.so > > -- -- Found Boost program_options library: /usr/local/lib/libboost_program_options.so > > -- -- Found Boost regex library: /usr/local/lib/libboost_regex.so > > -- Found BLAS and LAPACK: /usr/lib/liblapack.so;/usr/lib/libblas.so > > -- Configuring done > > -- Generating done > > -- Build files have been written to: /home/Pde2016/libs/nektar++/build > > Pde2016@ubuntu-1:~/libs/nektar++/build$ make > > [ 2%] Built target scotch-6.0.4 > > [ 2%] Built target tinyxml-2.6.2 > > [ 2%] Built target zlib-1.2.7 > > [ 2%] Built target boost > > [ 11%] Built target LibUtilities > > [ 14%] Built target StdRegions > > [ 17%] Built target SpatialDomains > > [ 19%] Built target LocalRegions > > [ 20%] Built target Collections > > [ 26%] Built target MultiRegions > > [ 28%] Built target GlobalMapping > > [ 35%] Built target FieldUtils > > [ 38%] Built target NekMeshUtils > > [ 38%] Linking CXX executable NekMesh > > ../../library/LibUtilities/libLibUtilities.so.4.5.0: undefined reference to `TiXmlDocument::TiXmlDocument(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' > > ../../library/LibUtilities/libLibUtilities.so.4.5.0: undefined reference to `operator>>(std::istream&, TiXmlNode&)' > > ../../library/SpatialDomains/libSpatialDomains.so.4.5.0: undefined reference to `TiXmlElement::SetAttribute(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' > > ../../library/LibUtilities/libLibUtilities.so.4.5.0: undefined reference to `operator<<(std::ostream&, TiXmlNode const&)' > > ../../library/SpatialDomains/libSpatialDomains.so.4.5.0: undefined reference to `TiXmlElement::TiXmlElement(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' > > collect2: error: ld returned 1 exit status > > utilities/NekMesh/CMakeFiles/NekMesh.dir/build.make:583: recipe for target 'utilities/NekMesh/NekMesh' failed > > make[2]: *** [utilities/NekMesh/NekMesh] Error 1 > > CMakeFiles/Makefile2:262: recipe for target 'utilities/NekMesh/CMakeFiles/NekMesh.dir/all' failed > > make[1]: *** [utilities/NekMesh/CMakeFiles/NekMesh.dir/all] Error 2 > > Makefile:140: recipe for target 'all' failed > > make: *** [all] Error 2 > > > > Thanks! All the best! > > > > Wenjie Liu > > Lecturer, > > Department of Mathematics, > > Harbin Institute of Technology > > _______________________________________________ > > Nektar-users mailing list > > Nektar-users(a)imperial.ac.uk > > https://mailman.ic.ac.uk/mailman/listinfo/nektar-users

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Compile the last version nektar++ shows link errors
by liuwenjie＠hit.edu.cn 06 Jun '18

06 Jun '18

Dear all I compile the last version nektar++, used g++ 8.0.1 and cmake 3.11.2 in 64 ubuntu. I tried some suggestions. It still shows the following link errors. Can you given me some advice? Very thanks! Pde2016@ubuntu-1:~/libs/nektar++/build$ cmake -DCMAKE_INSTALL_PREFIX=/home/Pde2016/Bin/nektar-4.5.0 .. -- Found TinyXML: /usr/local/lib/libtinyxml.a -- Build Scotch: /home/Pde2016/libs/nektar++/build/ThirdParty/dist/lib/libscotch.a -- Found Zlib: /usr/lib/x86_64-linux-gnu/libz.so (version 1.2.8) -- Searching for Boost: -- -- Found Boost thread library: /usr/local/lib/libboost_thread.so -- -- Found Boost iostreams library: /usr/local/lib/libboost_iostreams.so -- -- Found Boost filesystem library: /usr/local/lib/libboost_filesystem.so -- -- Found Boost system library: /usr/local/lib/libboost_system.so -- -- Found Boost program_options library: /usr/local/lib/libboost_program_options.so -- -- Found Boost regex library: /usr/local/lib/libboost_regex.so -- Found BLAS and LAPACK: /usr/lib/liblapack.so;/usr/lib/libblas.so -- Configuring done -- Generating done -- Build files have been written to: /home/Pde2016/libs/nektar++/build Pde2016@ubuntu-1:~/libs/nektar++/build$ make [ 2%] Built target scotch-6.0.4 [ 2%] Built target tinyxml-2.6.2 [ 2%] Built target zlib-1.2.7 [ 2%] Built target boost [ 11%] Built target LibUtilities [ 14%] Built target StdRegions [ 17%] Built target SpatialDomains [ 19%] Built target LocalRegions [ 20%] Built target Collections [ 26%] Built target MultiRegions [ 28%] Built target GlobalMapping [ 35%] Built target FieldUtils [ 38%] Built target NekMeshUtils [ 38%] Linking CXX executable NekMesh ../../library/LibUtilities/libLibUtilities.so.4.5.0: undefined reference to `TiXmlDocument::TiXmlDocument(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' ../../library/LibUtilities/libLibUtilities.so.4.5.0: undefined reference to `operator>>(std::istream&, TiXmlNode&)' ../../library/SpatialDomains/libSpatialDomains.so.4.5.0: undefined reference to `TiXmlElement::SetAttribute(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' ../../library/LibUtilities/libLibUtilities.so.4.5.0: undefined reference to `operator<<(std::ostream&, TiXmlNode const&)' ../../library/SpatialDomains/libSpatialDomains.so.4.5.0: undefined reference to `TiXmlElement::TiXmlElement(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' collect2: error: ld returned 1 exit status utilities/NekMesh/CMakeFiles/NekMesh.dir/build.make:583: recipe for target 'utilities/NekMesh/NekMesh' failed make[2]: *** [utilities/NekMesh/NekMesh] Error 1 CMakeFiles/Makefile2:262: recipe for target 'utilities/NekMesh/CMakeFiles/NekMesh.dir/all' failed make[1]: *** [utilities/NekMesh/CMakeFiles/NekMesh.dir/all] Error 2 Makefile:140: recipe for target 'all' failed make: *** [all] Error 2 Thanks! All the best! Wenjie Liu Lecturer, Department of Mathematics, Harbin Institute of Technology

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compile nektar++ shows link errors
by liuwenjie＠hit.edu.cn 04 Jun '18

04 Jun '18

Dear all I compile the last version nektar++, used g++ 8.0.1 and cmake 3.11.2 in 64 ubuntu. It shows the following link errors. Can you help me fix it? Very thanks! [ 42%] Building CXX object utilities/NekMesh/CMakeFiles/NekMesh.dir/ProcessModules/ProcessVarOpti/ElUtil.cpp.o [ 42%] Linking CXX executable NekMesh ../../library/LibUtilities/libLibUtilities.so.4.5.0: undefined reference to `TiXmlDocument::TiXmlDocument(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' ../../library/LibUtilities/libLibUtilities.so.4.5.0: undefined reference to `operator>>(std::istream&, TiXmlNode&)' ../../library/SpatialDomains/libSpatialDomains.so.4.5.0: undefined reference to `TiXmlElement::SetAttribute(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' ../../library/LibUtilities/libLibUtilities.so.4.5.0: undefined reference to `operator<<(std::ostream&, TiXmlNode const&)' ../../library/SpatialDomains/libSpatialDomains.so.4.5.0: undefined reference to `TiXmlElement::TiXmlElement(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' collect2: error: ld returned 1 exit status utilities/NekMesh/CMakeFiles/NekMesh.dir/build.make:583: recipe for target 'utilities/NekMesh/NekMesh' failed make[2]: *** [utilities/NekMesh/NekMesh] Error 1 CMakeFiles/Makefile2:262: recipe for target 'utilities/NekMesh/CMakeFiles/NekMesh.dir/all' failed make[1]: *** [utilities/NekMesh/CMakeFiles/NekMesh.dir/all] Error 2 Makefile:140: recipe for target 'all' failed make: *** [all] Error 2 Thanks! All the best! Wenjie Liu Lecturer, Department of Mathematics, Harbin Institute of Technology

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fixed mass flux in channel flow
by Sandeep Pandey 01 Jun '18

01 Jun '18

Hello all, I am a newbie to Nektar++ and I validated turbulent channel flow DNS with the standard DNS database. For now, the flow was driven by the constant pressure gradient. As a next step, I want to drive flow with such forcing so that I have constant mass flux at every time step. The forcing should take the following form to achieve the constant mass flux: *dpdx(time)= dpdx(time-1) -[ 0.3*(massFlowRef (time=0) - 2*massFlow (time) + massFlow(time-1) ) / (Ly*Lz*dt)]* where; *massflow *should be volume integrated value. Does anyone has already implemented such forcing? Or does anyone any idea? I am familiar with ./library/SolverUtils/Forcing, but any hint in the specific direction will be very useful to me. Thanks and have a nice weekend! Sandeep

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