- Nektar-users - imperial.ac.uk

Import OpenFOAM mesh to Nektar++
by Marc Goldbach 26 May '22

26 May '22

******************* 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 All, I am attempting to import an existing OpenFOAM mesh into Nektar++ (I am trying to avoid having to recreate this mesh from scratch). I do this by exporting the mesh from OpenFOAM as a VTK format, and then use gmsh to import the VTK files (There is one file for each boundary plus the volume mesh), and then write the files as a .msh file. Finally, I use NekMesh to read the .msh file and convert to an .xml format with: NekMesh -v -m linkcheck wmc.msh wmcMesh.xml This doesn't return any errors, but it seems that the mesh is not generated properly since the wmcMesh.xml file shows the boundaries as having zero faces: 12 <COMPOSITE> 13 <C ID="1"> F[0] </C> 14 <C ID="2"> F[0] </C> 15 <C ID="3"> F[0] </C> 16 <C ID="4"> F[0] </C> 17 <C ID="5"> F[0] </C> 18 <C ID="6"> F[0] </C> 19 <C ID="7"> F[0] </C> 20 <C ID="8"> H[0-972399] </C> 21 </COMPOSITE> 22 <DOMAIN> C[8] </DOMAIN> 23 </GEOMETRY> 24 <Metadata> 25 <Provenance> 26 <Hostname>str-c37.uncc.edu</Hostname> 27 <NektarVersion>5.2.0</NektarVersion> 28 <Timestamp>26-May-2022 11:51:40</Timestamp> 29 </Provenance> 30 <NekMeshCommandLine>-v -m linkcheck wmc.msh wmcMesh.xml </NekMeshCommandLine> 31 </Metadata> 32 <EXPANSIONS> 33 <E COMPOSITE="C[8]" NUMMODES="4" TYPE="MODIFIED" FIELDS="u,v,w,p" /> 34 </EXPANSIONS> 35 </NEKTAR> However, the log seems to show Nektar++ does recognize the boundary elements: [InputGmsh] Reading Gmsh file: 'wmc.msh' [InputGmsh] Cannot find corresponding element face for 2D element 0 [InputGmsh] This element has 4 vertex [InputGmsh] This element has 4 edges [InputGmsh] Finished reading mesh. [InputGmsh] - Element dimension : 3 [InputGmsh] - Space dimension : 3 [InputGmsh] - No. of nodes : 1014073 [InputGmsh] - No. of 3D elements : 972400 [InputGmsh] - No. of boundary elements : 82536 [InputGmsh] - Elapsed time: 45.646s. [ProcessLinkCheck] Checking boundary-element links. [ProcessLinkCheck] Cannot find corresponding element face for 2D element 0 [ProcessLinkCheck] This element has 4 vertex [ProcessLinkCheck] This element has 4 edges [ProcessLinkCheck] - Elapsed time: 30.1317s. [OutputNekpp] Writing Nektar++ file 'wmcMesh.xml' [OutputNekpp] - Elapsed time: 46.8262s. Any suggestions on how this can be corrected, or how to import the mesh from OpenFOAM? Thanks in advance for any help. *Marc Goldbach* PhD Student, Department of Mechanical Engineering University of North Carolina at Charlotte

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Some suggestions and details I would like to add to the Windows Installing instructions of Nektar++
by Mo, Haifan 06 May '22

06 May '22

******************* 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 recently downloaded Nektar++ on my windows computer, and I would say it is the most "difficult to install" software I have ever downloaded, the instruction for the installing process for Linux was unclear so I gave up (I used Ubuntu focal), if you could record the process and post it on YouTube it would be very helpful, there is one on YouTube but it does not seem to be official instruction. Fortunately, the software is available on Windows so I tried to follow your instruction, it was difficult as well, but still manageable. There are some details not mentioned in the instruction (like the use of git and how to call Visual Studio in the command prompt), I have attached a file to explain them.

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Overshoot in instantaneous pressure near curved boundary
by 曹勇 05 May '22

05 May '22

******************* 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 all, I recently started to use Nektar++ v5.0.3. I would like to simulate the incompressible flow past a smooth circular cylinder at Re=3900. The case is classic and widely studied. The test case used 3345 macro-elements in 2D plane (x-y plane). 70 edges are distributed on the cylinder boundary. The other direction (z direction) is solved by Fourier mode. For the purpose of test, a short spanwise length is set, like Lz=0.2. The results of instantaneous velocity field seems smooth near the boundary of circular cylinder. However, the instantaneous pressure field showed overshoot (or numerical oscillation?) between two neighboring macro-elements. I attached an example in the email. In order to manifest the overshoot, the visualization uses the magnitude of pressure gradient. For solving this problem, I conducted some additional tests by either adding macro-elements along the cylinder boundary or increasing the number of points of Gauss quadrature. Both methods smoothened the instantaneous pressure field around the cylinder boundary. However, neither removed the overshoot completely. It will be appreciated if anyone could give suggestions. Thank you very much in advance. Yong Cao

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The usage of scalargrad module
by 张俊达 04 May '22

04 May '22

******************* 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 all: I am new to Nektar++, I have used Nektar++ to simulate a simple steady state 2-D thermal conduction problem, where I define the boundary conditions as one for temperature determination (Dirichlet conditions) and one for heat flow density determination (Neumann conditions). When I want to use the scalargrad module in fieldconvert to calculate the gradient of a boundary to get the heat flow density in where the temperature is determined. It said I need a xml file to process the fld file. I reference the “5.5.11 Extract a boundary region: extract module” in user-guide, use extract module in nekmesh to get the xml file of the boundary and get the .dat file. But the data seems wrong for the u_scalar_gradient data is same in each point and the value is the temperature value that I defined in this boundary. So could you tell me if I choose the right xml file or which operation I miss out? How can I get the gradient on the boundary or nearby? By the way, I meet the segmentation fault when I use some fieldconvert module. if there any way can help me make it report which step that occur this fault? Many thanks for your help! Best! Junda Zhang

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Nektar++ in cylindrical coordinates
by Wang, Zhicheng 24 Apr '22

24 Apr '22

******************* 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'm wondering if the current version Nektar++ incompressible flow solver can do simulation in cylindrical coordinates ? I found documents from the following website that shows it can, but didn't find the corresponding piece of code. https://prism.ac.uk/wp-content/uploads/2019/10/grocco_nektar.pdf Best regards Zhicheng Wang

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Meshing of random packed spheres
by Daniel Lester 04 Apr '22

04 Apr '22

Hi Nektar Users, I’m not a Nektar user but I am considering using this code for a project involving computation of flows across the interface of a porous medium comprised of random packed spheres (RPS) - i.e. flow within the medium, the boundary layer and the turbulent bulk. Previous finite volume models of RPS involved smoothing of the cusp-shaped geometry at the contact points between spheres. Would this geometry be feasible to mesh and run in nektar if the # of spheres was order 100's, or would this be getting too fiddly/complex? Any feedback greatly appreciated, cheers Daniel

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Q3D simulations around cylinders
by Alessandro Alberto de Lima 26 Mar '22

26 Mar '22

******************* 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. How are you? I am running some cases of flow around cylinders and, for the case of Re = 1000, I get curious results. The lift force history showed strange oscillations like presented in the attached images. I am using SVV with 64 Fourier modes in z direction for the simulations and my mesh was developed following the descriptions found in a recent publication involving nektar++ and OpenFOAM. I believe that the mesh is not the problem. There is another option for pressure solution and force calculations? Have you any idea about what I'm doing wrong? Thank you! Alessandro

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monitor the torsional force of a 2-D cylinder in the new version code nektar ++ 5.10
by hongfu2233 15 Mar '22

15 Mar '22

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Stability convergence criteria
by Matt Duran 15 Mar '22

15 Mar '22

******************* 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 Nektar++ community, I recently have been running an adjoint stability simulation and am interested in the vortex shedding mode. >From the Strouhal number found in the literature I know the eigenmode of interest is the one highlighted below with a magnitude of 0.97 and a frequency of 0.731. [image: image.png][image: image.png] I have tried using a Krylov space of 40 and instructing Nektar to wait for the 20 modes with the highest magnitude to converge but I have no luck in getting the specific mode of interest to converge. I was wondering whether there was some way I could narrow down the convergence criteria so the specific mode I need will converge, rather than these other 20 modes I’m getting. I have tried to also converge modes by the highest imaginary part but I can’t seem to get the specific mode I need. Thank you, Matt Duran PhD student University of Central Florida

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Incompressible Navier-Stokes Solver
by Dongmyung Suh 03 Mar '22

03 Mar '22

******************* 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 All, I am studying Nektar++ by following the tutorial of Incompressible Navier-Stokes Solver in ( https://www.nektar.info/notebooks//tutorials/basics-incns-solver/) I wrote the condition file (mysession.xml) following the direction in the website. But it didn't work. I guess that there were some info missing. When I checked session2d.xml <https://www.nektar.info/notebooks//tutorials/basics-incns-solver/session2d.…> , there was also some error. So I couldn't see the correct working file. How can I get the session file? Please let me know. Thanks, Dongmyung Suh

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