October 2020 - Nektar-users

discontinuous results when using ariable polynomial order
by 王昭予 09 Nov '20

09 Nov '20

******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Dear Prof. Sherwin Thanks for your reply. There is a problem is when I use variable polynomial order in the field, the results near the boundary between 2 domains with different polynomial order cant be smoothed by C0projection module. So how can I handle the discontinuous results in this case? Many thanks, Zhaoyu Wang Shanghai Jiao Tong University

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how to monitor the heat flux or momentum flux along some boundary region.
by ztdepyahoo 27 Oct '20

27 Oct '20

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Nektar++ install help!
by Octavio Morales 26 Oct '20

26 Oct '20

******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Hi Nektar team, I've been trying to install Nektar++ in my Ubuntu 20.04 LTS but nothing seems to work. If someone have succeeded at installing Nektar++ in this Ubuntu version, could you please tell me what you did so it can work? I installed the C++ compiler, CMake, BLAS/LAPACK and Scotch and nothing. Any help will be extremely appreciated!!

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How to compute the heat flux along a boundary region in nektar
by Professor Ding、 25 Oct '20

25 Oct '20

******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Dear sir: I am using netkar 4.5 for natural convection problem. I want to know how to monitor the heat flux or momentum flux along some boundary region. Regards | | Professor Ding、 | | ztdepyahoo(a)163.com | 签名由网易邮箱大师定制

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Nektar++-5.0.0 installation on Linux
by Fatih Ertinaz 24 Oct '20

24 Oct '20

******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Hello everyone After a couple of unsuccessful attempts, I decided to write here for some help. I've tried to build Nektar++-5.0.0 from its source using two different environments: - On a machine that has Ubuntu-16.04, GCC-9.3.0 and OpenMPI-4.0.4 - On a Docker environment (hosted on the Ubuntu machine) with CentOS-7, GCC-4.8.5 and OpenMPI-4.0.4 I initially tried using Docker because I'm preparing containers for a project I'm developing at the moment. I had some environment related troubles with GCC-7.3.0, so decided to stick with the default GCC which is 4.8. I don't have the logs right now but build failed with something like: > MMFAdvection.cpp:945:35: error: 'dF' may be used uninitialized in this > function [-Werror=maybe-uninitialized I thought this might be due to the old GCC version (which now I think it's not), and decided to complete the installation using the new GCC suite on my laptop which is the system I shared in the first item above. However, these new attempts also have failed. This my build script: > export PATH=/opt/openmpi-4.0.4/bin:$PATH > export LD_LIBRARY_PATH=/opt/openmpi-4.0.4/lib:$LD_LIBRARY_PATH > cmake .. \ # I'm in src/build > -DCMAKE_INSTALL_PREFIX=/opt/nektar++-5.0.0 \ > -DNEKTAR_BUILD_DEMOS=ON \ > -DNEKTAR_BUILD_LIBRARY=ON \ > -DNEKTAR_BUILD_SOLVERS=ON \ > -DNEKTAR_BUILD_UTILITIEs=ON \ > -DNEKTAR_USE_MPI=ON \ > -DNEKTAR_USE_OPENBLAS=ON \ > -DNEKTAR_USE_BOOST=ON \ > -DNEKTAR_USE_SCOTCH=ON \ > -DTHIRDPARTY_BUILD_OPENBLAS=ON \ > -DTHIRDPARTY_BUILD_BOOST=ON \ > -DTHIRDPARTY_BUILD_SCOTCH=ON > > make install This is the shorter script which I've excluded FFTW, HDF5, ARPACK, PETSC and METIS. When HDF5 is enabled, the build fails with: > [ 13%] Building CXX object > library/LibUtilities/CMakeFiles/LibUtilities.dir/BasicUtils/FieldIOHdf5.cpp.o > /home/fertinaz/nektar/nektar++-5.0.0/library/LibUtilities/BasicUtils/FieldIOHdf5.cpp: > In member function ‘virtual void > Nektar::LibUtilities::FieldIOHdf5::v_Import(const string&, > std::vector<std::shared_ptr<Nektar::LibUtilities::FieldDefinitions> >&, > std::vector<std::vector<double> >&, > Nektar::LibUtilities::FieldMetaDataMap&, const Nektar::Array<Nektar::OneD, > int>&)’: > /home/fertinaz/nektar/nektar++-5.0.0/library/LibUtilities/BasicUtils/FieldIOHdf5.cpp:1028:31: > error: implicitly-declared > ‘Nektar::LibUtilities::FieldIOHdf5::OffsetHelper& > Nektar::LibUtilities::FieldIOHdf5::OffsetHelper::operator=(const > Nektar::LibUtilities::FieldIOHdf5::OffsetHelper&)’ is deprecated > [-Werror=deprecated-copy] > 1028 | decompsToOffsets[i] = running; > | ^~~~~~~ So I've disabled HDF5 and a couple of others. Eventually, I want them too, but I wanted to use as little external libs as possible in the first step. Then initiated a new build which failed with the following error: > [ 20%] Building CXX object > library/SpatialDomains/CMakeFiles/SpatialDomains.dir/MeshGraph.cpp.o > /home/fertinaz/nektar/nektar++-5.0.0/library/SpatialDomains/MeshGraph.cpp: > In member function ‘void > Nektar::SpatialDomains::MeshGraph::SetExpansionsToEvenlySpacedPoints(int)’: > /home/fertinaz/nektar/nektar++-5.0.0/library/SpatialDomains/MeshGraph.cpp:1529:54: > error: implicitly-declared ‘Nektar::LibUtilities::BasisKey& > Nektar::LibUtilities::BasisKey::operator=(const > Nektar::LibUtilities::BasisKey&)’ is deprecated [-Werror=deprecated-copy] > 1529 | expIt->second->m_basisKeyVector[i] = bkeynew; Error due to "bkeynew" assignment repeats itself a couple of times and then the build exits with: > *cc1plus: all warnings being treated as errors <<<* > library/SpatialDomains/CMakeFiles/SpatialDomains.dir/build.make:254: > recipe for target > 'library/SpatialDomains/CMakeFiles/SpatialDomains.dir/MeshGraph.cpp.o' > failed > make[2]: *** > [library/SpatialDomains/CMakeFiles/SpatialDomains.dir/MeshGraph.cpp.o] > Error 1 > CMakeFiles/Makefile2:2271: recipe for target > 'library/SpatialDomains/CMakeFiles/SpatialDomains.dir/all' failed > make[1]: *** [library/SpatialDomains/CMakeFiles/SpatialDomains.dir/all] > Error 2 > Makefile:140: recipe for target 'all' failed > make: *** [all] Error 2 See the line I've highlighted. All of these errors occur because "-Werror" flag is enabled. I know this is the right way of doing things, however on a large application like Nektar I'm not sure if it must be this strict. So the question is what would be the best solution to tackle those warnings? I'm planning to disable the "Werror" flag unless there is a better idea. Thank you Fatih Ertinaz

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Visualizing deforming and moving geometry in post-processing
by Debbahi Saad 21 Oct '20

21 Oct '20

******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Dear Nektar users, I have launched a few runs of the cylinder example demonstrating the global mapping approach for geometry deformation, using the IncNavierStokesSolver, however when trying to visualize the deformation under Paraview or Tecplot the post-processor shows no geometry alteration? Please notice that I've used the Hdf5 output format for parallel run. and batch converted the *.chk files using FieldConvert which definitely uses the same XML session file to generate the .plt and .vtu files. If it's normal to see no geometry alteration, could there be a way to alter the geometry accordingly and obtain a model that visually deforms in the post-processor? Thanks to all of you, S. Debbahi

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Torque of a rotating body under crossflow
by Victor Hugo Santiago Peron 21 Oct '20

21 Oct '20

******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Hello all, I'm currently using the incompressible Navier-Stokes tool to measure the stability of bodies under torsional oscillation and I'm wondering if the IncNavierStokesSolver algorithm provides the value of the torque caused by the fluid in the body. Could you please provide me this information and, if possible, where to get it? Thanks in advance, Best regards. Victor Peron Department of Mechanical Engineering Escola Politécnica da Universidade de São Paulo

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MovingBody for fluid/structure interaction of rotating body?
by Yong Wang 17 Oct '20

17 Oct '20

******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Hello, I have simulated the vertical VIV of the bridge deck using the MovingBody approach, and it worked quite well. My current focus is about simulating the rotational VIV, so I wonder if the coordinate system transformation method for rotating bodies (Li et al, 2000) has been implemented in Nektar++. Li, L., Sherwin, S.J., Bearman, P.W., 2002. A moving frame of reference algorithm for fluid/structure interaction of rotating and translating bodies. International Journal for Numerical Methods in Fluids 38, 187–206. https://doi.org/10.1002/fld.216 Best wishes, Yong wang Ph.D. Student National Wind Institute Texas Tech University Lubbock, TX, United States

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Installation help.
by Octavio Morales 17 Oct '20

17 Oct '20

******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Hi, I am having troubles to install Nektar. I attached what appears in my terminal when I try to compile using -make install- and my configuration in -ccmake ../- Really hope you can help me, thank you so much!

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Question regarding compatibility with Ubuntu 20.04.1 LTS
by Octavio Morales 15 Oct '20

15 Oct '20

******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Hi, I am currently working on Ubuntu 20.04.21 LTS. Is Nektar 5.0.0. compatible with my Ubuntu version? If it is not, what should i do to use Nektar?

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