- Nektar-users - imperial.ac.uk

Some problems with BiGlobal Floquet analysis
by 张洪福 15 Jun '15

15 Jun '15

Hi All, I encounter some problems with Nektar++. I want to calculate the eigenmode of a period field using BiGlobal Floquet analysis. 1, I have gotten a series base flow file (xx_1.bse, xx_2.bse ......). The Residual error of base period flow (long enough) , L 2 error (variable u), is about 10, and others are o(10^-1). *Is the result **convergence*? (i also got the lift force of the bluff body, and it shows period smoothly ) 2, The total structural quadrangular element of the 2D mesh is about 14000, order of P is 8, the Re number is 4000. The external flow is similar to the example in User Guide 8.6.12 (version 4.0.1), but i simulate a plan-like bluff body instead of cylinder. when i run the "mpirun -np 4 IncNavierStokesSolver XX.xml " , the XX_0.chk folder is generate, but it stay all day long in that state (no error, no respones). Simultaneously, I run "IncNavierStokesSolver XX.xml" ,i.e., using single processor, it works well (although slowly). Anyone can tell me why and what should I do? 3, How can I get the corresponding eigenmode of eigenvalue in .evl file? 4, I am a newbie, would anyone gives me some advises in my simulation? I will appreciate! PS, the part of .xml content (base flow): </SOLVERINFO> <PARAMETERS> TimeStep = 0.0001 NumSteps = 100000 IO_CheckSteps = 10000 IO_InfoSteps = 100 Re = 4000 Kinvis = 0.775/4000 </PARAMETERS>

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Coupled incompressible solver with periodic conditions and regular mesh
by Stanisław Gepner 09 Jun '15

09 Jun '15

Hi, I think I found a problem when importing Gmsh meshes into Nektar. This happens if I try to use the coupled solver and the periodic BC. Works with VelocityCorrection, or if BC are standard D / N. What I do: 1. Using the geometry in channel.geo create a mesh in Gmsh. This is a rectangular channel. I use Transfinite and Recombine to get a structured quad mesh. 2. I use MeshConvert with paralign to generate the channel.xml 3. If run with the attached cond2D.xml Nektar fails in AssemblyMap.cpp line 284, with "These values should never be the same" The problem is persistent with other recombined/transfinite meshes. If any of you is aware of how I could try to avoid the problem, I would be obliged. Regards, Stan Gepner

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Problem when using MPI
by Stanisław Gepner 28 May '15

28 May '15

Dear All, Has any of you have ever had any problems with GSMPI when in parallel? I am having some problems running Nektar in parallel on SHARCNET (https://www.sharcnet.ca) I have run Nektar in parallel before on other clusters (https://c-cfd.meil.pw.edu.pl/hpc/) and had no problems using it. Let me describe it: If I do: IncNavierStokesSolver geom.xml cond.xml all is good, If I do (also through the pbs system) mpirun -n 2 IncNavierStokesSolver geom.xml cond.xml I get a Segmentation fault. If I try to delay process communication (e.g. by loading prepartitioned meshes) I can see some output. So I think the problem starts with the first MPI send/recive. That is why think there is something with the GSMPI since it wraps the MPI communication (right?). I have already tried with different compilers (intel and gcc), different boost distributions etc. Are you aware if there might be any problems with certain OpenMPI versions, or something like this? Best Regards, Stan Gepner

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Stability analysis - import base flow from other solver
by Rohner Adrian 28 May '15

28 May '15

Dear nektar-users, I want to perform stability analysis with nektar and I started with some Examples like the cylinder case. Now, the plan was to proceed as follows: 1. Flow simulation of symmetric model(to prevent the oscillations) with CFX or COMSOL in the higher RE-Range(instable region), think for the cylinder case it would be 45-160(2d) 2. Next step would be to import flow and pressure field into nektar and perform stability analysis Has anyone done similar things? How about importing, interpolation and so on? And if it is not possible to use data from another solver how can I do the defined progress In nektar? Best regards, adrian Adrian Rohner Projektmitarbeiter | BSc FHO in Maschinentechnik HSR Hochschule für Technik Rapperswil IET Institut für Energietechnik | +41 55 222 4263 | www.iet.hsr.ch<http://www.iet.hsr.ch/>

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About Periodic Conditions
by YU Jian 27 May '15

27 May '15

Dear All, I am trying to using the periodic condition within the CompressibleFlowSolver. I have tested the IsentropicVortex case with periodic conditions imposed at all boundaries. The xml file(attached with this mail) was generated with MeshConvert from a Gmesh file. I found out that in the <COMPOSITE> part, the listing order of the faces on a pair of periodic boundaries must be one-to-one correspondance, otherwise the boundary condition will not be applied correctly. However, MeshConvert seems not to be able to ensure the correct orders. For example, Wrong(generated directly by MeshConvert): <C ID="2"> F[14,4,31,23] </C> <C ID="3"> F[8,17,26,33] </C> <C ID="4"> F[1,7,20,25] </C> <C ID="5"> F[18,13,34,30] </C> <C ID="6"> F[0,6,11,16] </C> <C ID="7"> F[24,28,32,35] </C> Correct(modified manually): <C ID="2"> F[14,4,31,23] </C> <C ID="3"> F[17,8,33,26] </C> <C ID="4"> F[1,7,20,25] </C> <C ID="5"> F[13,18,30,34] </C> <C ID="6"> F[0,6,11,16] </C> <C ID="7"> F[24,28,32,35] </C> I further checked the MeshConvert , and found out that at line 339 of the file 'OutputNekpp.cpp', there is a comment "Ensure that this composite is not used for periodic BCs!". Does this mean that MeshConvert can not be used when periodic BCs exist? Thank you in advance! Best wishes, Jian YU <?xml version="1.0" encoding="utf-8" ?> <NEKTAR> <GEOMETRY DIM="3" SPACE="3"> <VERTEX> <V ID="0">0.00000000e+00 -5.00000000e+00 0.00000000e+00</V> <V ID="1">5.00000000e+00 -5.00000000e+00 0.00000000e+00</V> <V ID="2">5.00000000e+00 0.00000000e+00 0.00000000e+00</V> <V ID="3">0.00000000e+00 0.00000000e+00 0.00000000e+00</V> <V ID="4">0.00000000e+00 -5.00000000e+00 5.00000000e+00</V> <V ID="5">5.00000000e+00 -5.00000000e+00 5.00000000e+00</V> <V ID="6">5.00000000e+00 0.00000000e+00 5.00000000e+00</V> <V ID="7">0.00000000e+00 0.00000000e+00 5.00000000e+00</V> <V ID="8">1.00000000e+01 -5.00000000e+00 0.00000000e+00</V> <V ID="9">1.00000000e+01 0.00000000e+00 0.00000000e+00</V> <V ID="10">1.00000000e+01 -5.00000000e+00 5.00000000e+00</V> <V ID="11">1.00000000e+01 0.00000000e+00 5.00000000e+00</V> <V ID="12">5.00000000e+00 5.00000000e+00 0.00000000e+00</V> <V ID="13">0.00000000e+00 5.00000000e+00 0.00000000e+00</V> <V ID="14">5.00000000e+00 5.00000000e+00 5.00000000e+00</V> <V ID="15">0.00000000e+00 5.00000000e+00 5.00000000e+00</V> <V ID="16">1.00000000e+01 5.00000000e+00 0.00000000e+00</V> <V ID="17">1.00000000e+01 5.00000000e+00 5.00000000e+00</V> <V ID="18">0.00000000e+00 -5.00000000e+00 1.00000000e+01</V> <V ID="19">5.00000000e+00 -5.00000000e+00 1.00000000e+01</V> <V ID="20">5.00000000e+00 0.00000000e+00 1.00000000e+01</V> <V ID="21">0.00000000e+00 0.00000000e+00 1.00000000e+01</V> <V ID="22">1.00000000e+01 -5.00000000e+00 1.00000000e+01</V> <V ID="23">1.00000000e+01 0.00000000e+00 1.00000000e+01</V> <V ID="24">5.00000000e+00 5.00000000e+00 1.00000000e+01</V> <V ID="25">0.00000000e+00 5.00000000e+00 1.00000000e+01</V> <V ID="26">1.00000000e+01 5.00000000e+00 1.00000000e+01</V> </VERTEX> <EDGE> <E ID="0"> 0 1 </E> <E ID="1"> 1 2 </E> <E ID="2"> 2 3 </E> <E ID="3"> 3 0 </E> <E ID="4"> 0 4 </E> <E ID="5"> 1 5 </E> <E ID="6"> 2 6 </E> <E ID="7"> 3 7 </E> <E ID="8"> 4 5 </E> <E ID="9"> 5 6 </E> <E ID="10"> 6 7 </E> <E ID="11"> 7 4 </E> <E ID="12"> 1 8 </E> <E ID="13"> 8 9 </E> <E ID="14"> 9 2 </E> <E ID="15"> 8 10 </E> <E ID="16"> 9 11 </E> <E ID="17"> 5 10 </E> <E ID="18"> 10 11 </E> <E ID="19"> 11 6 </E> <E ID="20"> 2 12 </E> <E ID="21"> 12 13 </E> <E ID="22"> 13 3 </E> <E ID="23"> 12 14 </E> <E ID="24"> 13 15 </E> <E ID="25"> 6 14 </E> <E ID="26"> 14 15 </E> <E ID="27"> 15 7 </E> <E ID="28"> 9 16 </E> <E ID="29"> 16 12 </E> <E ID="30"> 16 17 </E> <E ID="31"> 11 17 </E> <E ID="32"> 17 14 </E> <E ID="33"> 4 18 </E> <E ID="34"> 5 19 </E> <E ID="35"> 6 20 </E> <E ID="36"> 7 21 </E> <E ID="37"> 18 19 </E> <E ID="38"> 19 20 </E> <E ID="39"> 20 21 </E> <E ID="40"> 21 18 </E> <E ID="41"> 10 22 </E> <E ID="42"> 11 23 </E> <E ID="43"> 19 22 </E> <E ID="44"> 22 23 </E> <E ID="45"> 23 20 </E> <E ID="46"> 14 24 </E> <E ID="47"> 15 25 </E> <E ID="48"> 20 24 </E> <E ID="49"> 24 25 </E> <E ID="50"> 25 21 </E> <E ID="51"> 17 26 </E> <E ID="52"> 23 26 </E> <E ID="53"> 26 24 </E> </EDGE> <FACE> <Q ID="0"> 0 1 2 3</Q> <Q ID="1"> 0 5 8 4</Q> <Q ID="2"> 1 6 9 5</Q> <Q ID="3"> 2 6 10 7</Q> <Q ID="4"> 3 7 11 4</Q> <Q ID="5"> 8 9 10 11</Q> <Q ID="6"> 12 13 14 1</Q> <Q ID="7"> 12 15 17 5</Q> <Q ID="8"> 13 16 18 15</Q> <Q ID="9"> 14 16 19 6</Q> <Q ID="10"> 17 18 19 9</Q> <Q ID="11"> 2 20 21 22</Q> <Q ID="12"> 20 23 25 6</Q> <Q ID="13"> 21 23 26 24</Q> <Q ID="14"> 22 24 27 7</Q> <Q ID="15"> 10 25 26 27</Q> <Q ID="16"> 14 28 29 20</Q> <Q ID="17"> 28 30 31 16</Q> <Q ID="18"> 29 30 32 23</Q> <Q ID="19"> 19 31 32 25</Q> <Q ID="20"> 8 34 37 33</Q> <Q ID="21"> 9 35 38 34</Q> <Q ID="22"> 10 35 39 36</Q> <Q ID="23"> 11 36 40 33</Q> <Q ID="24"> 37 38 39 40</Q> <Q ID="25"> 17 41 43 34</Q> <Q ID="26"> 18 42 44 41</Q> <Q ID="27"> 19 42 45 35</Q> <Q ID="28"> 43 44 45 38</Q> <Q ID="29"> 25 46 48 35</Q> <Q ID="30"> 26 46 49 47</Q> <Q ID="31"> 27 47 50 36</Q> <Q ID="32"> 39 48 49 50</Q> <Q ID="33"> 31 51 52 42</Q> <Q ID="34"> 32 51 53 46</Q> <Q ID="35"> 45 52 53 48</Q> </FACE> <ELEMENT> <H ID="0"> 0 1 2 3 4 5 </H> <H ID="1"> 6 7 8 9 2 10 </H> <H ID="2"> 11 3 12 13 14 15 </H> <H ID="3"> 16 9 17 18 12 19 </H> <H ID="4"> 5 20 21 22 23 24 </H> <H ID="5"> 10 25 26 27 21 28 </H> <H ID="6"> 15 22 29 30 31 32 </H> <H ID="7"> 19 27 33 34 29 35 </H> </ELEMENT> <COMPOSITE> <C ID="1"> H[0-7] </C> <C ID="2"> F[14,4,31,23] </C> <C ID="3"> F[8,17,26,33] </C> <C ID="4"> F[1,7,20,25] </C> <C ID="5"> F[18,13,34,30] </C> <C ID="6"> F[0,6,11,16] </C> <C ID="7"> F[24,28,32,35] </C> </COMPOSITE> <DOMAIN> C[1] </DOMAIN> </GEOMETRY> <EXPANSIONS> <E COMPOSITE="C[1]" NUMMODES="15" FIELDS="rho,rhou,rhov,rhow,E" TYPE="MODIFIED" /> </EXPANSIONS> <CONDITIONS> <PARAMETERS> FinTime = 10. TimeStep = 0.002 NumSteps = 0 IO_CheckSteps = 500 IO_InfoSteps = 1 Gamma = 1.4 pInf = 101325 rhoInf = 1.225 uInf = 0.1 vInf = 0.0 wInf = 0.0 CFL = 0 </PARAMETERS> <SOLVERINFO> </SOLVERINFO> <VARIABLES> <V ID="0"> rho </V> <V ID="1"> rhou </V> <V ID="2"> rhov </V> <V ID="3"> rhow </V> <V ID="4"> E </V> </VARIABLES> <BOUNDARYREGIONS> C[2] C[3] C[4] C[5] C[6] C[7] </BOUNDARYREGIONS> <BOUNDARYCONDITIONS> <REGION REF="1"> </REGION> <REGION REF="2"> </REGION> <REGION REF="3"> </REGION> <REGION REF="4"> </REGION> <REGION REF="5"> </REGION> <REGION REF="6"> </REGION> </BOUNDARYCONDITIONS>   </CONDITIONS> </NEKTAR>

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Update on Nektar++ workshop
by David Moxey 26 May '15

26 May '15

Dear all, Just a quick update on the Nektar++ workshop for those that are yet to register! The event is now definitely going ahead. You can find the most recent information here on location and accommodation options: http://sherwinlab.ae.ic.ac.uk/nektar-workshop-2015/ As the Doodle poll was just to ascertain the level of interest, in order to keep track of everyone, we have replaced it with a registration form through EventBrite, which you can access here: https://www.eventbrite.co.uk/e/nektar-workshop-2015-tickets-16799728440 I hope that you are able to attend and look forward to seeing you there. 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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weak form of diffusion term for 1d homogeneous problem
by Zhicheng Wang 23 May '15

23 May '15

Hi all, I'm trying to implement a stabilized method for incompressible N-S equation. Basically, the form of the stabilized term looks like nu*L_u, where nu is the the artificial viscosity which is varying across quadratue points, L_u is the Laplacian operation of a velocity component. My plan is using the explicit scheme to discretize this stabilized term to avoid assembling the system matrix at every time step. I'd like to add the stabilized term to the right hand side in the viscous correction stage of the velocity correction scheme. However I'm not very clear how to implement it using Nektar++ for the case of 3DHomogeneous1D . Here I attached a piece of my current code, hope someone could help me to correct the mistakes. // velocity_array[0] stored the first component of velocity vector in Fourier space // z direction is homogeneous // nu stored artificial viscosity // np is number of quadrature points in a 2D plane // nc is number of SEM coefficients in a 2D plane Vmath::Vadd(np*num_planes, nu ,1, velocity_array[0],1,velocity_array[0],1); m_fields[1]->PhysDeriv(0,velocity_array[0],velocity_derv[0]); // gradient in x direction m_fields[1]->PhysDeriv(1,velocity_array[0],velocity_derv[1]); // gradient in y direction cnt = 0; cnt1 = 0; 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, &velocity_derv[0]+cnt, &wkCoef1[0] +cnt1); m_fields[1]->GetPlane(i)->IProductWRTDerivBase(1, &velocity_derv[1]+cnt, &wkCoef1[0]+cnt1); m_fields[1]->GetPlane(i)->IProductWRTBase(tmp1 = &velocity_array[0]+i*np, &wkCoef2[0]+i*nc,MultiRegions::eGlobal); Vmath::Smul(nc, beta, &wkCoef2[0] + i*nc, 1, &wkCoef2[0]+ i*nc, 1); cnt += np; cnt1 += nc; } Vmath::Vadd(NumTotCoeffs,wkCoef0,1,wkCoef1,1,visc,1); Vmath::Vadd(NumTotCoeffs,wkCoef0,1,wkCoef2,1,visc,1);

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User Guide
by Kamil ÖZDEN 13 May '15

13 May '15

Dear All, I want to learn how to generate the necessary Fourier coefficients to use in Womersley Equation for generating pulsatile inlet flow boundary condition. However, I couldn't see any detail about this issue in the user-guide I downloaded from www.nektar.info. As far as I learned these issues are detailed in the user-guide of latest version of Nektar++ downladed from git-repository. This user guide seems in the nektar/docs/user - guide folder as *.tex file. I tried to compile this file but I always get the following error. /*user-guide.tex error line 377: File `../../VERSION.tex' not found. \titlepage */How can I reach the user-guide including information about the issues above. Regards, Kamil

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Mesh order on curved boundary
by Zhicheng Wang 30 Apr '15

30 Apr '15

Hi there, I'd like to use nektar++ to simulate 3d flow over a circular cylinder. but I'm feeling a little confused about the mesh order of curved boundaries. My puzzle is as follow: If SEM basis is 4-order polynomial, and the mesh, generated by Gmsh, is 3-order. it means the order of base function is higher than mesh order of mesh. is there any inconsistency in this case ? zhicheng

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FieldConvert error from calculating vorticity and Qcriterion
by Zhicheng Wang 30 Apr '15

30 Apr '15

Hi nektar++ users and developers, I 'm using the latest nektar++ version. However when running the TurbChFl_3DH1D.xml example and using FieldConvert calculating vorticity or Qcriterion, I got errors as "ERROR: Element u_33 is 0 from dgetrf". I have checked the velocity and pressure field, it is correct, so if there is some inconsistency in FieldConvert for 1D homogeneous problem?

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