May 2022 - Nektar-users - imperial.ac.uk

Cannot connect to cloud resources
by 董智康 30 May '22

30 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 trying to connect to your cloud resources Jupyter notebook (the link from tutorial). But it seems like the server is not responded. I’m not sure if you close your cloud resources or there are some problems with my network. Thanks, Zhikang Dong

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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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