- Nektar-users - imperial.ac.uk

Question about Stream function module for 2D, Incompressible Flow
by Seyedi, Hadi 24 Feb '20

24 Feb '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, This is Hadi Seyedi from Michigan State University. I am a PhD student at ME department and I am using NEKTAR++ to perform my 2D incompressible N-S simulations. When I want to use the Stream function module in FiledConvert, I am getting the below error. I could use the other modules easily, but this one (streamfunction module) doesn't work for my cases. Would you please help me in this regard? Thank You in advance, Hadi Error: Fatal : Level 0 assertion violation Variable index out of range. terminate called after throwing an instance of 'Nektar::ErrorUtil::NekError' what(): Level 0 assertion violation Variable index out of range. [Hadi-PC:05963] *** Process received signal *** [Hadi-PC:05963] Signal: Aborted (6) [Hadi-PC:05963] Signal code: (-6) [Hadi-PC:05963] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x12890)[0x7f86a3e80890] [Hadi-PC:05963] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0xc7)[0x7f86a3abbe97] [Hadi-PC:05963] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x141)[0x7f86a3abd801] [Hadi-PC:05963] [ 3] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x8c957)[0x7f86a46cf957] [Hadi-PC:05963] [ 4] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x92ab6)[0x7f86a46d5ab6] [Hadi-PC:05963] [ 5] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x92af1)[0x7f86a46d5af1] [Hadi-PC:05963] [ 6] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x92d24)[0x7f86a46d5d24] [Hadi-PC:05963] [ 7] /home/hadi/NEKTAR/nektar++-5.0.0/build/dist/lib64/libLibUtilities.so.5.0.0(+0x1b8c32)[0x7f86a5516c32] [Hadi-PC:05963] [ 8] /home/hadi/NEKTAR/nektar++-5.0.0/build/dist/lib64/libLibUtilities.so.5.0.0(+0x1b9058)[0x7f86a5517058] [Hadi-PC:05963] [ 9] /home/hadi/NEKTAR/nektar++-5.0.0/build/dist/lib64/libFieldUtils.so.5.0.0(_ZN6Nektar10FieldUtils5Field17SetUpFirstExpListEib+0xec5)[0x7f86a5f8f305] [Hadi-PC:05963] [10] /home/hadi/NEKTAR/nektar++-5.0.0/build/dist/lib64/libFieldUtils.so.5.0.0(_ZN6Nektar10FieldUtils16ProcessCreateExp7ProcessERN5boost15program_options13variables_mapE+0x43d)[0x7f86a5fb61cd] [Hadi-PC:05963] [11] FieldConvert(_Z9RunModuleSt10shared_ptrIN6Nektar10FieldUtils6ModuleEERN5boost15program_options13variables_mapEb+0x3f)[0x55f8f55093af] [Hadi-PC:05963] [12] FieldConvert(main+0x172c)[0x55f8f550587c] [Hadi-PC:05963] [13] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7f86a3a9eb97] [Hadi-PC:05963] [14] FieldConvert(_start+0x2a)[0x55f8f5508d3a] [Hadi-PC:05963] *** End of error message *** Aborted (core dumped)

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Regarding installing the Nektar++
by pavan yadav 12 Feb '20

12 Feb '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 struggling with installation of Nektar++ on ubuntu 16.04. Can you please suggest a way to install it? Regards, Pavan

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Installing Nektar++ in Windows 10
by m_moayeri＠sbu.ac.ir 11 Feb '20

11 Feb '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 all, I am a PhD candidate of scientific computing at Shahid Beheshti university, Iran. I am trying to install Nektar++ in Windows. I follow up the instructions in user guide, but I encounter with the following errors when I try to do 11th steps of installing Nektar++: "C:\University\PhD\Nektar++\nektar++-5.0.0\builds\INSTALL.vcxproj" (default target) (1) -> "C:\University\PhD\Nektar++\nektar++-5.0.0\builds\ALL_BUILD.vcxproj" (default target) (3) -> "C:\University\PhD\Nektar++\nektar++-5.0.0\builds\boost.vcxproj" (default target) (8) -> (CustomBuild target) -> collect2.exe : error : ld returned 1 exit status [C:\University\PhD\Nektar++\nektar++-5.0.0\builds\boost.vcxpr oj] collect2.exe : error : ld returned 1 exit status [C:\University\PhD\Nektar++\nektar++-5.0.0\builds\boost.vcxpr oj] collect2.exe : error : ld returned 1 exit status [C:\University\PhD\Nektar++\nektar++-5.0.0\builds\boost.vcxpr oj] collect2.exe : error : ld returned 1 exit status [C:\University\PhD\Nektar++\nektar++-5.0.0\builds\boost.vcxpr oj] Does any one know what are the error related to and help me? Best regards, Mahdi

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Nektar++ Developer Guide
by 张滕飞 11 Feb '20

11 Feb '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 all, My name is Tengfei Zhang and I am an assistant professor at Shanghai Jiao Tong University, China. Currently I am trying to implement new models in the Nektar++ platform by making revisions in the source code. Problem is, the developer guide (pdf version) that I can find on Gitlab seems to be outdated, and the re-compilation using latex files does not work properly and the generated pdf file misses important information. I am wondering if anyone could kindly share a newest version of the developer guide (in pdf format)? My email address is zhangtengfei(a)sjtu.edu.cn. Or does anyone know a download link for the updated developer guide file? I really appreciate it. Best regards, Tengfei Zhang Assistant Professor School of Mechanical Engineering Shanghai Jiao Tong University

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error MSB6006: "cmd.exe" exited with code 1
by Silvia Ceccacci (HDR) 23 Jan '20

23 Jan '20

******************* This email from 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 all, I am Silvia Ceccacci, from Macquarie University. I am trying to install Nextar on Windows but I am having some troubles with it. Here my questions: 1) Is MS Visual Studio 2019 working for Nektar? I can see the 2015 is preferred and I have tried to use it but it gave me some issues. The 2019 version seems to work fine when I generate the build scripts with CMake. 2) When I issue the command: msbuild INSTALL.vcxproj /p:Configuration=Release on the Visual Studio 2019 terminal, I get this error: error MSB6006: "cmd.exe" exited with code 1 Could you please help me understand what I should be doing and how to solve this problem? Thank you. Kind regards Silvia

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Up-to-date build from source on IC HPC cluster
by Thibaut Appel 20 Jan '20

20 Jan '20

Hello, I was just wondering how people compile Nektar++ from source on the IC cluster these days and if there are any recommended adjustments compared with that this link says https://www.nektar.info/nektar-cx1/ It is 4 years old but the instructions still work, it seems I'm able to compile Nektar++ with module load mpi/intel-2019.6.166 module load intel-suite/2017.6 module load fftw/3.3.3-double module load flex/2.6.4 module load scotch/6.0.4 module load boost/1.66.0 CC=mpicc CXX=mpicxx cmake -DNEKTAR_USE_FFTW=ON -DNEKTAR_USE_MKL=ON DNEKTAR_USE_MPI=ON -DNEKTAR_USE_SYSTEM_BLAS_LAPACK=OFF -DNEKTAR_TEST_FORCEMPIEXEC=ON -DCMAKE_CXX_FLAGS="-std=c++11 -O3 -xSSE4.2 -axAVX,CORE-AVX-I,CORE-AVX2" -DCMAKE_C_FLAGS="-O3 -xSSE4.2 -axAVX,CORE-AVX-I,CORE-AVX2" .. Would you recommend any change with respect to newer packages or better practice for efficiency? Thanks for the support, Thibaut

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Re: [Nektar-users] Aeroacoustics using cwipi in nektar++-5
by Kilian Lackhove 15 Jan '20

15 Jan '20

******************* This email from 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 Nitish, Great to hear it works for you, i will add the note to the userguide then. Regarding the implementation: The Coupling writes its received data directly into the m_Forcing array. Unfortunately, the Upate method in ForcingBody.cpp would allocate a new array each time step. By using FIELDFORCETIMEFCN, the m_hasTimeFcnScaling flag is set to true and Update is called only once during initialization (which is fine), so the arrays stay the same. The condition with the "x y z t" does not check the expression of the CouplingSource function, but its variables, which are set elsewhere in the code and cannot be altered by the user IIRC. So that has nothing to do with the Coupling. Cheers, Kilian Am 14.01.20 um 07:03 schrieb Nitish Arya: > Dear Kilian, > > I looked into the code and found that when no value is provided to an > expression, it adds "x y z t" to it. In the ForcingBody.cpp the > coupling force is read if there is no value (or the other way round, I > am still confused) provided for the CouplingSource function. But the > following worked for me. > > <FUNCTION NAME="CouplingSource"> > <E VAR="p,u,v,w" VALUE =" "/> > </FUNCTION> > </CONDITIONS> > <FORCING> > <FORCE TYPE="Field"> > <FIELDFORCE> CouplingSource <FIELDFORCE/> > <FIELDFORCETIMEFCN> 1.0 </FIELDFORCETIMEFCN> > </FORCE> > </FORCING> > > I am able to read the source terms as well as the base fields now. > > regards, > Nitish > > > On Tue, 14 Jan, 2020, 1:24 AM Kilian Lackhove, <kilian(a)lackhove.de > <mailto:kilian@lackhove.de>> wrote: > > Hi Nitish, > > i am glad to hear you got the setup working. Regarding the > forcing, you > need to set > > <FIELDFORCETIMEFCN> 1.0 </FIELDFORCETIMEFCN> > > (see e.g. solvers/DummySolver/Tests/Dummy_3DCubeCwipi_0.xml for an > example) > > This is a workaround for an incompatibility between the way the > forcing > is implemented and how the coupling works. Let me know if it > worked for > you so i can add this piece if info to the userguide. > > Cheers, > > Kilian > > > Am 09.01.20 um 16:16 schrieb Nitish Arya: > > Dear Kilian, > > > > Thank you very much for your suggestion. The cwipi functionality in > > the new release really solved my problem. I also successfully > compiled > > the openfoam interface [3] with the acoustic solver in nektar. The > > reception of base fields (u0,v0,w0) is absolutely fine. However, > when > > I tried receiving the source terms (F_0_p, F_0_u, F_0_v, F_0_w), > the > > corresponding fields are not reflected in nektar. The source > terms are > > zero everywhere (since they were initialized to zero in the > > configuration file). This could mean that after the transfer > they are > > being modified to the value in the configuration file. Am I missing > > something? > > > > I have also attached the conditions file in the mail. > > > > > > > > regards, > > Nitish > > > > >

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Problem to solve the Forward Step test
by Victoria Korchagova 14 Jan '20

14 Jan '20

******************* This email from 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 want to use Nektar++ Compressible Flow Solver for modelling of supersonic flows and testing of different techniques of the shock-capturing in future. I have tried to run a simple test Forward Step (Woodward, Collela) by CompressibleFlowSolver, but some problems have appeared. The simulation is stable only for CFL = 0.001. Increasing of CFL causes a vacuum on the first step. My mesh resolution is 8 cells per step height. My settings: <EXPANSIONS> <E COMPOSITE="C[5]" NUMMODES="3" FIELDS="rho,rhou,rhov,E" TYPE="MODIFIED" /> </EXPANSIONS> <CONDITIONS> <PARAMETERS> TimeStep = 0 CFL = 0.001 FinTime = 4.0 NumSteps = 0 IO_CheckSteps = 1000 IO_InfoSteps = 500 Gamma = 1.4 rhoInf = 1.0 uInf = 3.0 vInf = 0.0 pInf = 1.0 / Gamma mu = 1e-12 cInf = sqrt(Gamma * pInf / rhoInf)  Skappa = -1.3 Kappa = 0.2 mu0 = 1.0 </PARAMETERS> <SOLVERINFO> </SOLVERINFO> <VARIABLES> <V ID="0"> rho </V> <V ID="1"> rhou </V> <V ID="2"> rhov </V> <V ID="3"> E </V>  </VARIABLES> <BOUNDARYREGIONS> C[1] 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="0" /> <D VAR="E" VALUE="pInf / (Gamma - 1) + 0.5 * rhoInf * (uInf * uInf + vInf * vInf)" />  </REGION> <REGION REF="1"> <D VAR="rho" USERDEFINEDTYPE="PressureOutflowNonReflective" VALUE="rhoInf" /> <D VAR="rhou" USERDEFINEDTYPE="PressureOutflowNonReflective" VALUE="rhoInf*uInf" /> <D VAR="rhov" USERDEFINEDTYPE="PressureOutflowNonReflective" VALUE="0" /> <D VAR="E" USERDEFINEDTYPE="PressureOutflowNonReflective" VALUE="pInf / (Gamma - 1) + 0.5 * rhoInf * (uInf * uInf + vInf * vInf)" />  </REGION> <REGION REF="2"> <D VAR="rho" USERDEFINEDTYPE="Wall" VALUE="0" /> <D VAR="rhou" USERDEFINEDTYPE="Wall" VALUE="0" /> <D VAR="rhov" USERDEFINEDTYPE="Wall" VALUE="0" /> <D VAR="E" USERDEFINEDTYPE="Wall" VALUE="0" />  </REGION> <REGION REF="3"> <D VAR="rho" USERDEFINEDTYPE="Wall" VALUE="0" /> <D VAR="rhou" USERDEFINEDTYPE="Wall" VALUE="0" /> <D VAR="rhov" USERDEFINEDTYPE="Wall" VALUE="0" /> <D VAR="E" USERDEFINEDTYPE="Wall" VALUE="0" />  </REGION> </BOUNDARYCONDITIONS> <FUNCTION NAME="InitialConditions"> <E VAR="rho" VALUE="rhoInf" /> <E VAR="rhou" VALUE="rhoInf * uInf" /> <E VAR="rhov" VALUE="rhoInf * vInf" /> <E VAR="E" VALUE="pInf / (Gamma - 1) + 0.5 * rhoInf * (uInf * uInf + vInf * vInf)" />  </FUNCTION> </CONDITIONS> I’ll be very thankful for help! -- Best regards, Victoria Korchagva

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Re: [Nektar-users] Aeroacoustics using cwipi in nektar++-5
by Kilian Lackhove 13 Jan '20

13 Jan '20

******************* This email from 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 Nitish, i am glad to hear you got the setup working. Regarding the forcing, you need to set <FIELDFORCETIMEFCN> 1.0 </FIELDFORCETIMEFCN> (see e.g. solvers/DummySolver/Tests/Dummy_3DCubeCwipi_0.xml for an example) This is a workaround for an incompatibility between the way the forcing is implemented and how the coupling works. Let me know if it worked for you so i can add this piece if info to the userguide. Cheers, Kilian Am 09.01.20 um 16:16 schrieb Nitish Arya: > Dear Kilian, > > Thank you very much for your suggestion. The cwipi functionality in > the new release really solved my problem. I also successfully compiled > the openfoam interface [3] with the acoustic solver in nektar. The > reception of base fields (u0,v0,w0) is absolutely fine. However, when > I tried receiving the source terms (F_0_p, F_0_u, F_0_v, F_0_w), the > corresponding fields are not reflected in nektar. The source terms are > zero everywhere (since they were initialized to zero in the > configuration file). This could mean that after the transfer they are > being modified to the value in the configuration file. Am I missing > something? > > I have also attached the conditions file in the mail. > > > > regards, > Nitish > >

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Regarding our paper in JFM
by Abhishek Kumar 13 Jan '20

13 Jan '20

******************* This email from 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 friends, I am happy tell that our paper titled "Mixed baroclinic convection in a cavity" is now published in JFM. We have extensively used incompressible solver with a buoyant scalar of Nektar++. I have attached a copy of the paper in this email. I would like to thank the entire team of Nektar++ for the support during this work and giving me an opportunity to present this result during the last Nekar++ workshop. With regards Abhishek -- --------------------------------------------------------------------------------------- Abhishek Kumar Research Associate Centre for Fluid and Complex Systems Coventry University, Coventry CV15FB United Kingdom Webpage: https://abhishekkir.wixsite.com/website Email # ac7600(a)coventry.ac.uk, abhishek.kir(a)gmail.com Phone: +44 24 7765 9150 Mobile: +44 7464026494 ---------------------------------------------------------------------------------------

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