October 2024 - Nektar-users

Failed to read nek5000 data
by Wei He 04 Nov '24

04 Nov '24

******************* 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++ developers and users, I am planing to use 3D flow datas generated by nek5000. When I run the command on a centos machine, the process fails with errors, as shown below: FieldConvert roCyl_half0.f00100 cyl.fld -------------------------------------------------------------------------- WARNING: There was an error initializing an OpenFabrics device. Local host: master Local device: mlx5_0 -------------------------------------------------------------------------- Field contains unknown variable: X [master:42932] *** Process received signal *** [master:42932] Signal: Aborted (6) [master:42932] Signal code: (-6) [master:42932] [ 0] /lib64/libpthread.so.0(+0xf630)[0x7f85cfcf4630] [master:42932] [ 1] /lib64/libc.so.6(gsignal+0x37)[0x7f85cf94d387] [master:42932] [ 2] /lib64/libc.so.6(abort+0x148)[0x7f85cf94ea78] [master:42932] [ 3] /share/home/user1/nektar++/build/dist/lib64/libFieldUtils.so.5.6.0(_ZN6Nektar10FieldUtils12InputNek50009v_ProcessERN5boost15program_options13variables_mapE+0xe70)[0x7f85d3db2590] [master:42932] [ 4] FieldConvert[0x41e615] [master:42932] [ 5] FieldConvert[0x41b47e] [master:42932] [ 6] /lib64/libc.so.6(__libc_start_main+0xf5)[0x7f85cf939555] [master:42932] [ 7] FieldConvert[0x41dad2] [master:42932] *** End of error message *** Aborted (core dumped) While I also tried a 2D case on my laptop, it neither doesn't pass the procession. I wonder if I did the correct things, and thank you in advance! regards, Wei FieldConvert cylinder2D0.f00100 cyl.fld Field contains unknown variable: X [Harqin:55513] *** Process received signal *** [Harqin:55513] Signal: Abort trap: 6 (6) [Harqin:55513] Signal code: (0) [Harqin:55513] [ 0] 0 libsystem_platform.dylib 0x00000001878fe584 _sigtramp + 56 [Harqin:55513] [ 1] 0 libsystem_pthread.dylib 0x00000001878cdc20 pthread_kill + 288 [Harqin:55513] [ 2] 0 libsystem_c.dylib 0x00000001877daa30 abort + 180 [Harqin:55513] [ 3] 0 libFieldUtils.5.5.0.dylib 0x0000000100a784dc _ZN6Nektar10FieldUtils12InputNek50009v_ProcessERN5boost15program_options13variables_mapE + 5284 [Harqin:55513] [ 4] 0 FieldConvert 0x00000001002f7b5c _Z9RunModuleNSt3__110shared_ptrIN6Nektar10FieldUtils6ModuleEEERN5boost15program_options13variables_mapEb + 820 [Harqin:55513] [ 5] 0 FieldConvert 0x00000001002f24e8 main + 18272 [Harqin:55513] [ 6] 0 dyld 0x0000000187543154 s tart + 2476 [Harqin:55513] *** End of error message *** zsh: abort FieldConvert cylinder2D0.f00100 cyl.fld

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Nektar++ 5.7.0 Released.
by Chris Cantwell 31 Oct '24

31 Oct '24

Dear all, We are pleased to announce the release of Nektar++ v5.7.0. As always, if you encounter any problems please feel free to contact us on the mailing list nektar-users(a)imperial.ac.uk. You can also report bugs and issues on our issue tracker (https://gitlab.nektar.info/nektar/nektar/-/issues) This release includes a range of new features and improvements over the 5.6.0 release: **Library** - Modified MatrixFreeOp library switch initialisation to use BOOST_PP (!1794) - Fix memory-leak with LowEnergyBlock preconditioner for time-updated matrices (!1627) - Fix Fourier expansion integration weights are related test (!1803) - Introduced the MatrixFree implementation for the PhysInterp1DScaled operator and tidying up MatrixFreeOps (!1812) - Separate MeshGraph input/output functions into a new class (!1778) - Added checkpoint file writing start time in the fieldconvert filter (!1789) - Fix fieldconvert filter incorrect boundary values (!1789) - Fix numerical precision issues with filters OutputStartTime (!1789) - Fix AdaptiveSFD for MPI (!1821) - Fix interpolation on manifold (!1840) - Fix IterativeStaticCond when using absolute tolerance (!1850) - Fix deadlock by scotch with multi-threading support (!1853) - Fixed L2norm for FilterError (!1871) - Fix variable p in tetrahedrons (!1881) - Fix BwdTrans for Pyr with var P (!1886) - Allow wrapper array around a existing raw pointer (!1848) - Tweaked some long tests to make them faster (!!1918) **IncNavierStokesSolver** - Fix initial and boundary conditions in the moving reference frame (!1692, ! 1820) - Fix memory-leak for the Mixed_CG_Discontinuous projection when initializing the traceMep (!1806) - Add synthetic turbulence generation for the incompressible solver (!1664) - Fix a uninitialized parameter in VCS (!1880) **ShallowWaterSolver** - Implement implicit time-discritization (!1784) **CompressibleSolver** - Add synthetic turbulence generator for the compressible solver (!1859) **NekMesh** - Added revolve module (!1825) - Fix Prism Reordering in Process PerAlign (!1899) - Extend quality measures in ProcessJac and add histogram generation(!1751) - Reducing run time of some tests in NekMesh(!1922) - Extend quality measures in ProcessJac and add histogram generation (!1751) - Reducing run time of some tests in NekMesh (!1922) - Added a reader for the CGNS input format (!1889) **FieldConvert** - Add vortexinducedvelocity module to compute the vortex-induced velocity (! 1824) - Add a module to transform coordinates and vectors for the moving reference frame method (!1830) **Miscellaneous** - Use std::stod instead of boost::lexical_cast<NekDouble> (!1819) **Documentation** - Add initial documentation for the IncNavierStokesSolver (!1822) - Updated the supported packages in Userguid (!1904) - Added a example for RayleighBenardConvection in the user-guide for IncNS (! 1919) - Fix some typos in tutorials (!1929) **CI and Packaging** - Debian 10 (BUSTER) is no longer supported (!1902) - Support is added for Ubuntu Noble Numbat and droped for Bionic Beaver (!1910) - Removed Fedora 35/36, added Fedora 39/40 (!1909) Cheers, Chris -- Chris Cantwell Reader in Computational Engineering Department of Aeronautics Imperial College London South Kensington Campus London SW7 2AZ Tel: +44 (0)20 759 45050 Email: c.cantwell(a)imperial.ac.uk www.imperial.ac.uk/people/c.cantwell

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Error when restarting - ReynoldsStresses
by Daniel Garcia 24 Oct '24

24 Oct '24

******************* 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, how are you? I'm receiving an error (not specified) when restarting a 3D simulation which has the ReynoldsStresses filter activated. I don't get the error when the simulation is 2D nor when I use the AverageFields filter. So it just happens when I use the ReynoldsStresses filter in the Quasi-3D simulation. I'm also solving a scalar equation. Would it be a bug in this specific setup condition? I tried versions 5.4 and 5.5. Or does anyone know a workaround? I'm doing separated averages to combine later with the respective FieldConvert module for now. Thank you very much, Daniel.

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[IncNavierStokes+passive scalar]
by Tainá Gomes Rodovalho 22 Oct '24

22 Oct '24

******************* 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 Nectar++ users, I am analyzing the dispersion of a solute in an incompressible, laminar flow with a low Reynolds number using the IncNavierStokes solver with passive scalar transport. I've adapted the model from the Backward-facing step <https://doc.nektar.info/tutorials/latest/flow-stability/bfs/flow-stability-…> tutorial with an additional infusion point in the upper region of the channel, particularly within the step region. However, I've encountered negative concentration values in simulations. To address this, I activated SVV True (second test), although I had a slight reduction in negative concentration regions. I also conducted mesh refinement (third test), which improved the situation but significantly increased computational costs. If possible, I would appreciate any suggestions and, additionally, I would like to know more about SVV. Thank you in advance. Best regards, Tainá Gomes Rodovalho P.S.: Attached are the concentration images for the tests performed.

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Compatibility with Star CCM+
by Kyle Neary (student) 19 Oct '24

19 Oct '24

******************* 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 Reader, I am a Masters student at the University of Glasgow, studying under Wrik Mallik, an avid user of Necktar++. Since I am a Masters student I opted to run my hybrid LES/APE CAA in Star CCM+. As I didn't want to run into trouble with OpenFOAM, as I've used Star a lot in the past. However, Star uses the same domain for the flow and APE acoustics (which is a bit silly). Due to time and computational power restraints, I would like to use a different domain for the acoustics than the flow. I am wondering if it is possible to export data from my field in StarCCM+ and use it within Nectar++? I can extract the Lamb Vector and the mean flow fields ect. Any help is much appreciated. Kind regards, Kyle

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WSS smoothing
by Guillermo Suárez 15 Oct '24

15 Oct '24

******************* 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, Is it possible to smooth the wall shear stress for a 2D case? Maybe using the C0Projection module? I have tried: FieldConvert -m wss:bnd=0:addnormals=1 test.xml test.fld test-wss.fld FieldConvert -m C0Projection test.xml test-wss_b0.fld test-C0Proj.fld However, test-wss.fld has only one dimensional basis, e.g., BASIS="Modified_A", and then the C0Projection fails. Thank you. Kind regards, Guillermo

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Wiggles in turbulent dissipation rate profile
by Xiao, Chengnian 13 Oct '24

13 Oct '24

******************* 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, Hope everyone is doing well! We keep seeing wiggles in our time- and plane-averaged profile for the turbulent dissipation rate \epsilon obtained from Nektar++ DNS results, as shown in the attached plot. They seem to appear whenever calculating profiles of second or higher order flow statistics involving velocity gradients, whereas the time-averaged flow profiles themselves look alright. From earlier posts, it seems that similar issues have also been reported by other users. Is there a way to alleviate the issue either through adapting the simulation or the postprocessing procedure, i.e. smoothing? Best regards, Cheng

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CAA in Nektar++
by feijian0919 10 Oct '24

10 Oct '24

******************* 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 professor, I am new to Nektar++, and I want to know something about the CAA in Nektar++. I see the recent paper which use the Antares library solved the FWH equation, but the paper "Variations with Mach number for gust–airfoil interaction noise" is not using FWH euqation, does Nektar++ itself have the ability to calculate noise problem? If so, can the nosie problem only be calculated by compressible solver? If the noise problem cannot be calculated by a compressible solver alone, are we going to use an AcousticSolver? And why the Riemann solver in AcousticSolver maybe_unused? With best regards

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Synthetic Eddy Method
by Alexander Schukmann 09 Oct '24

09 Oct '24

******************* 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, I remember that João had presented a Synthetic Eddy Generator at the last workshop and wanted to ask if it will appear with the next release. I would also like to know which methods are used and recommended by experienced Nektar users to generate inlet turbulence. Perhaps someone can say a few words about this. Many thanks in advance! All the bestAlex

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Memory leak with variable viscosity using Incompressible Navier-Stokes solver
by Debbahi Saad 03 Oct '24

03 Oct '24

******************* 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, Using a locally compiled version of nektar release 5.6.0 (which runs pretty well) to solve fully 3d plane Poiseuille flow geometry, I'm trying to add variable or temperature dependant viscosity, by defining a function in the nektar session file, to be evaluated and passed to VarCoeffMap D00, D11,D22 as suggested by M. R. Rouhanian, a while ago, indeed I've come to the conclusion that the Incompressible Navier-Stokes solvers use too much memory in a cumulative way without releasing it throughout the time advancement process. key points: - Correct behavior with constant viscosity. no problem, the IncNavierStokesSolver runs good - Source file modified: nektar-v5.6.0/solvers/IncNavierStokesSolver/EquationSystems/VelocityCorrectionScheme.cpp (*Line:890, VelocityCorrectionScheme::v_SolveViscous* function) - Monotonic memory usage increase when enabling variable viscosity through any of the possible 'nu' dependencies i.e.: nu(Temp),nu(x,y,z), nu(t), nu(x,y,z,t). - The memory usage reaches easily 10 gigabytes after 20 to 30 timesteps, obviously evenly spread over the 4 x IncNavierStokesSolver spawned processes, compared to 4x140MB=560MB for the constant viscosity case - The memory usage keeps increasing, never decreases, no release of the memory surplus from one timestep to the next, it just keeps adding up... - No crash the calculations do carry on, with a noticeable slowdown due to viscosity array update, however not usable from a practicality view point as any serious case simulation would claim few terabytes of leaked memory - Placing some "cout<<" printing arrays sizes show that the arrays involved do keep the same size no issues It seems to be a garbage collection issue or a missing destructor call that I'm not able to pinpoint or fix. Any help on this issue or suggestion to fix it are greatly appreciated, Thank you all in advance, wishing you all the best, Saad *Code details:* My *VelocityCorrectionScheme::v_SolveViscous* modified function (file attached herein) reads: void VelocityCorrectionScheme::v_SolveViscous( > const Array<OneD, const Array<OneD, NekDouble>> &Forcing, > const Array<OneD, const Array<OneD, NekDouble>> &inarray, > Array<OneD, Array<OneD, NekDouble>> &outarray, const NekDouble aii_Dt) > { > StdRegions::ConstFactorMap factors; > StdRegions::VarCoeffMap varCoeffMap = StdRegions::NullVarCoeffMap; > MultiRegions::VarFactorsMap varFactorsMap = MultiRegions > ::NullVarFactorsMap; > > AppendSVVFactors(factors, varFactorsMap); > ComputeGJPNormalVelocity(inarray, varCoeffMap); > /* > switch (coordim) > { > case 3: > Exp->GetCoords(xc0, xc1, xc2); > break; > default: > ASSERTL0(false, "Coordim not valid"); > break; > }*/ > > > //////////////////////////////////////////////////////////////////////////////// > /////////// Modifications to account for variable viscosity start > here:///////// > > int nuflag=0; //initialiazed to 0, fall back to constant viscosity if > nu(T) is not defined > time_t rawTime; > time(&rawTime); > NekDouble time = static_cast<NekDouble>(rawTime);//ensure time is of > NekDouble type > > // if the function nuOfT is defined in the session file, evaluate the > function and set variable viscosity > if(m_session->DefinesFunction("nuOfT")) > { > Array<OneD, NekDouble> xxc0,xxc1,xxc2;// declare NekDouble arrays to hold > coordinates > > int nqv;// total points > int coordim=3;// default dimension > LibUtilities::EquationSharedPtr nuOfTfunc; > nqv=m_fields[0]->GetTotPoints(); > > // allocate 0.0 valued arrays of totalpoints size, to receive the space > coordinates > xxc0 = Array<OneD, NekDouble>(nqv, 0.0); > xxc1 = Array<OneD, NekDouble>(nqv, 0.0); > xxc2 = Array<OneD, NekDouble>(nqv, 0.0); > > m_fields[0]->GetCoords(xxc0,xxc1,xxc2); > coordim=m_fields[0]->GetCoordim(0); > > Array<OneD,NekDouble> nuOfT(nqv,0.0);// 0.0 valued nekdouble array to > hold viscosity value at each point of space > nuOfTfunc=m_session->GetFunction("nuOfT",0); > > nuOfTfunc->Evaluate(xxc0,xxc1,xxc2,nuOfT);// evaluate the function nu(T) > varCoeffMap[StdRegions::eVarCoeffD00]=nuOfT;// assign the values of > viscosity for the three diagonal components (same) evaluated > varCoeffMap[StdRegions::eVarCoeffD11]=nuOfT;// at every point of space > using the decalred nu(T) function > varCoeffMap[StdRegions::eVarCoeffD22]=nuOfT; > > nuflag=1;// set the variable viscosity flag > > } > > // Solve Helmholtz system and put in Physical space > for (int i = 0; i < m_nConvectiveFields; ++i) > { > > // Add diffusion coefficient to GJP matrix operator (Implicit part) > if (m_useGJPStabilisation) > { > factors[StdRegions::eFactorGJP] = m_GJPJumpScale / m_diffCoeff[i]; > } > > // Setup coefficients for equation > factors[StdRegions::eFactorLambda] = 1.0 / aii_Dt / m_diffCoeff[i]; > if (nuflag==1) factors[StdRegions::eFactorTime]=time;//if the nuOfT nu(T) > function is defined set the tume factor, > //else continue with constant viscosity > > m_fields[i]->HelmSolve(Forcing[i], m_fields[i]->UpdateCoeffs(), factors, > varCoeffMap, varFactorsMap); > m_fields[i]->BwdTrans(m_fields[i]->GetCoeffs(), outarray[i]); > } > > > } > Sample function node from the xml session file: <FUNCTION NAME="nuOfT"> <E EVARS="c1" VALUE="Ra*Pr*c1" /> </FUNCTION>

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