- Nektar-users - imperial.ac.uk

NATIVE_LAPACK (ADVANCED) Not Found
by Tanmay Daripa 28 Jul '15

28 Jul '15

Dear All, I am a new user of Nektar++. I am having problem making the software using cmake. I have installed LAPACK, BLAS, MKL and every other that was required. On trying to cmake the software, the following error comes up : *CMake Error: The following variables are used in this project, but they are set to NOTFOUND.Please set them or make sure they are set and tested correctly in the CMake files:* *NATIVE_LAPACK (ADVANCED)* * linked by target "LibUtilities" in directory /home/user/Downloads/nektar++-4.0.1/library/LibUtilities* Any help is appreciated. Regards, Tanmay Daripa IIT Kharagpur

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Problem with ChanStability_Coupled.xml
by Péter Tamás Nagy 27 Jul '15

27 Jul '15

Dear All, I'm a new user of Nektar++. I would like to carry out some stability investigations. I have two questions in regard to the usage of the software. *1*. I wanted to compare the eigenvectors calculated by the unsteady and steady Navier-Stokes solvers, but I encountered a problem. I tried to run nektar++-4.0.1/solvers/IncNavierStokesSolver/Tests/ChanStability_Coupled.xml, but I got the following error: /"// //IncNavierStokesSolver ChanStability_Coupled.xml// //// //Fatal : Level 0 assertion violation// //Base flow must be defined for linearised forms.// //"/ Then I defined the BaseFlow as: /<FUNCTION NAME="BaseFlow">// // <E VAR="u" VALUE="-y*y+1" />// // <E VAR="v" VALUE="0" />// //</FUNCTION>/ The simulation was carried out in this case, but the results are wrong: /"IncNavierStokesSolver ChanStability_Coupled_mod.xml// // //=======================================================================// // Solver Type: Coupled Linearised NS// //=======================================================================// // Arnoldi solver type : Arpack// // Arpack problem type : LI// // Single Fourier mode : false // // Beta set to Zero : false // // Shift (Real,Imag) : 0,0// // Krylov-space dimension : 16// // Number of vectors : 2// // Max iterations : 500// // Eigenvalue tolerance : 1e-06// //======================================================// //Initial Conditions:// // - Field u: from file ChanStability_Coupled.rst// // - Field v: from file ChanStability_Coupled.rst// //Writing: "ChanStability_Coupled_mod_0.chk"// //Matrix Setup Costs: 2.37365// //Multilevel condensation: 1.29072// // Inital vector : input file // //Iteration 16, output: 0, ido=99 // //Converged in 16 iterations// //Converged Eigenvalues: 3// // 0 0 0 -nan -nan// //Writing: "ChanStability_Coupled_mod_eig_0"// // 1 0 0 -nan -nan// //Writing: "ChanStability_Coupled_mod_eig_1"// // 2 0 0 -nan -nan// //Writing: "ChanStability_Coupled_mod_eig_2"// //L 2 error (variable u) : 2.589// //L inf error (variable u) : 1// //L 2 error (variable v) : 0// //L inf error (variable v) : 0// //"//// /Maybe I misunderstood something, could you provide help with this issue? *2*. Is it somehow possible to export the pressure field of the eigenvectors or should I calculate it by the Poisson equation? In this case could you send me an example how can I calculate the derivatives of a field variable. I saw the function FldAddScalGrad but I don't know how can I use. I really appreciate any help. Best regards, Péter <mailto:nektar-users@imperial.ac.uk>

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GitLab updates and information
by David Moxey 26 Jul '15

26 Jul '15

Hi all, Just a couple of quick updates regarding GitLab. Firstly, tomorrow I will take GitLab down briefly at around 11am to do an update to the software. You should be aware that this will introduce a few visual interface changes. Secondly, we're there are quite a few long-term branches that haven't been developed for some time. So that we reduce the number of branches in the main repository to keep things a bit more manageable, these have now been split off into an archive repository: https://gitlab.nektar.info/archive/nektar Firstly, don't worry -- your source is almost certainly stored in your local git repository anyway, unless you deleted it purposefully (in which case you should remove it from the Nektar++ repository, too). There's a few ways that you can check out branches from the archive. The simplest is to just clone the archive repository with: $ git clone git@gitlab.nektar.info:archive/nektar nektar++-archive Alternatively, inside an existing repository, you can add the archive repository as an additional remote: $ cd nektar++ $ git remote add archive git@gitlab.nektar.info:archive/nektar.git $ git fetch archive Archived branches can then be checked out with: $ git checkout -t archive/feature/branch Cheers, Dave -- David Moxey (Research Associate) d.moxey(a)imperial.ac.uk | www.imperial.ac.uk/people/d.moxey Room 363, Department of Aeronautics, Imperial College London, London, SW7 2AZ, UK.

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Re: [Nektar-users] Postprocessing with matlab
by Hau, Jan-Niklas 24 Jul '15

24 Jul '15

Hi Rodrigo, Thanks for this hint. I'll take a look at it as well. Regards Jan Am 24.07.2015 2:59 nachm. schrieb Rodrigo Moura <r.moura13(a)imperial.ac.uk>: Hello Jan, Yes I agree with Spencer that probably the easiest thing would be to use the FieldConvert utility - please see the user manual. You can use a simple command like the following to probe the solution at a given list of points. ./FieldConvert -m interppoints:fromxml=cube.xml:fromfld=cube_t0.fld points.pts field_t0.dat I am sending attached an example for the list of points which should be in a given structure (check the attached points.pts file). You need the XML, the FLD and the PTS file to get a DAT file. Kind regards, Rodrigo .

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Postprocessing with matlab
by Jan-Niklas Hau 24 Jul '15

24 Jul '15

Dear all, is there a convenient way to import data written by nektar into matlab? Up till now I convert the output files to the tecplot format and then read them into matlab. Thank you very much in advance With best regards Jan Jan-Niklas Hau, M.Sc. TU Darmstadt, Department of Mechanical Engineering Chair of Fluid Mechanics Otto-Bernd-Str. 2 64287 Darmstadt, Germany Tel: +49 6151 16-5249 Fax: +49 6151 16-7061 Mail: hau(a)fdy.tu-darmstadt.de Web: http://www.fdy.tu-darmstadt.de/

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Turbulence intensity in the inflow
by Kamil ÖZDEN 19 Jul '15

19 Jul '15

Dear All, Is it possible to add turbulence intensity to the inflow for a pipe flow problem in Nektar++? Best Regards, Kamil

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Verbose option
by Kamil ÖZDEN 19 Jul '15

19 Jul '15

Dear All, In the user guide it is written that --verbose option is used to display extra info. However, there is no info about how this option is used, for example where should I write the --verbose option in such an mpirun execution? /*mpirun --mca btl_tcp_if_include 10.10.10.0/24 -np 128 /nektar++-4.0.0/build/solvers/IncNavierStokesSolver/IncNavierStokesSolver test.xml*/ And which extra information does --verbose option display? Best Regards, Kamil

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Time averaged output file
by Kamil ÖZDEN 19 Jul '15

19 Jul '15

Dear All, I want to ask that if is it possible to obtain time averaged output file (.fld or .chk) in Nektar++ to get time averaged contour plots? Best Regards, Kamil

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How to do post-process with BiGlobal Floquet analysis
by Hongfu Zhang 30 Jun '15

30 Jun '15

Hi All, I want to computethe eigenmode of a period field using BiGlobal Floquet analysis. The attachments are the related files. (Cyl.xml ---- the file simulates base flow; Cyl-sta.xml ----- the file calculate eigenvalue and eigenmode of the base flow; Cyl-sta.fld----the calculated (by Cyl-sta.xml) results ). I have used Cyl.xml, Cyl-sta.fld or Cyl-sta.xml, Cyl-sta.fld to generate .vtu files with FiedConvert, but all failed when I see the field with Paraview. Could anyone tell me how to do to see the results in Paraview. Thanks very much in advance! Best Regards Cyl.xml <https://drive.google.com/file/d/0B86D0j5lPOCDU3dNeWVLOF8xWUE/edit?usp=drive…> Cyl-sta.fld <https://drive.google.com/file/d/0B86D0j5lPOCDNFRCTWpKX3hFLWc/edit?usp=drive…> Cyl-sta.xml <https://drive.google.com/file/d/0B86D0j5lPOCDcUxHUENjcEEyYm8/edit?usp=drive…>

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explicit discretization for diffusion term in case of 3DHomoneneous1D case
by Zhicheng Wang 18 Jun '15

18 Jun '15

Hi All, I'd like to use explicit scheme to discretize the diffusion term in the case of 3DHomogeneous1D in continuous Galerkin projection framework. For example, I have an array u, which stores the value of first component of velocity vector in Fourier spoace. and I want to calculate the inner product (grad w, grad u), where w is the base function, grad is gradient operator. Could following code get the correct result? m_fields[0]->PhysDeriv(0,u ,u_derv[0]); // gradient in x direction m_fields[0]->PhysDeriv(1,u, u_derv[1]); // gradient in y direction for(unsigned int i=0; i<num_planes; ++i) { double beta = 2*M_PI*m_trans->GetK(i)/m_homoLen; beta *= beta; m_fields[0]->GetPlane(i)->IProductWRTDerivBase(0, &u _derv[0]+i*np, &wkCoef1[0] +i*nc); // m_fields[0]->GetPlane(i)->IProductWRTDerivBase(1, &u _derv[1]+i*np, &wkCoef1[0]+i*nc); m_fields[0]->GetPlane(i)->IProductWRTBase(tmp1 = &u[0]+i*np, &wkCoef2[0]+i*nc,MultiRegions::eGlobal); Vmath::Smul(nc, beta, &wkCoef2[0] + i*nc, 1, &wkCoef2[0]+ i*nc, 1); } Vmath::Vadd(NumTotCoeffs,wkCoef0,1,wkCoef1,1,diff,1); Vmath::Vadd(NumTotCoeffs,wkCoef0,1,wkCoef2,1,diff,1); // array diff stores the final diffusion value

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