May 2021 - Nektar-users - imperial.ac.uk

Fieldconvert question
by Vidhi Zala 19 Jul '21

19 Jul '21

******************* 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, I am wondering if there is a way to specify the number of points and basis type while converting chk -> vtu? I notice that irrespective of the quadrature points specified in the session file, the resulting vtu always has nummodes points. Any advice would be appreciated. Thanks V -- ,-~~-.___._. / | ' \ | |--------. Vidhi Zala ( ) 0 | | | School of Computing \_/-, ,----' | | | Scientific Computing and Imaging Institute ==== !_!-v---v--. University of Utah / \-'~; .--------. / __/~| ._-""|| | vidhi.zala(a)utah.edu =( _____|_|____||________| http://sci.utah.edu/people/vidhi.html I support Ruff Haven Crises Shelter for Homeless Pets <https://www.ruffhaven.org/donate>. Consider a donation today :)

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Stretching existing mesh using Nekmesh
by Vidhi Zala 31 May '21

31 May '21

******************* 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, I have a nekmesh question - Can I use nekmesh to take an existing 2D mesh in [image: [0,1]\times[0,1]] and stretch it t/o [image: [-10, 10] \times [-10,10]] ? Thanks V -- ,-~~-.___._. / | ' \ | |--------. Vidhi Zala ( ) 0 | | | School of Computing \_/-, ,----' | | | Scientific Computing and Imaging Institute ==== !_!-v---v--. University of Utah / \-'~; .--------. / __/~| ._-""|| | vidhi.zala(a)utah.edu =( _____|_|____||________| http://sci.utah.edu/people/vidhi.html I support Ruff Haven Crises Shelter for Homeless Pets <https://www.ruffhaven.org/donate>. Consider a donation today :)

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flow over airfoil
by Mahdi Erfanian Nakhchi 24 May '21

24 May '21

******************* 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 NEKTAR++ users, I have a quick question. I want to see if it is possible to use FFT to perform simulations over an airfoil with vortex generators on its surface. (Picture below) Or it can only be simulated in full 3D shape? Many thanks Mahdi Postdoc Research Fellow, Northumbria University [cid:561eba87-0128-4c9c-ad88-c1ec49d450c7] This message is intended solely for the addressee and may contain confidential and/or legally privileged information. Any use, disclosure or reproduction without the sender's explicit consent is unauthorised and may be unlawful. If you have received this message in error, please notify Northumbria University immediately and permanently delete it. Any views or opinions expressed in this message are solely those of the author and do not necessarily represent those of the University. Northumbria University email is provided by Microsoft Office365 and is hosted within the EEA, although some information may be replicated globally for backup purposes. The University cannot guarantee that this message or any attachment is virus free or has not been intercepted and/or amended.

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3D channel flow stability analysis not working in parallel?
by Xiao, Chengnian 17 May '21

17 May '21

******************* 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, I have been running nektar++-5.0.2 and trying the 3D stability analysis for the channel flow as described in the specific nektar tutorial. I used the session file "PPF_R10000_3D.xml" provided under the /Tests subdirectory of IncNavierStokesSolver, and obtained the same complex eigenvalues 0.518448+/-26.6405i as the tutorial when I ran the problem on a single processor. However, when I executed the same session on multiple (4) processors, the two eigenvalues upon convergence were different, namely -6.957 +/-1.34189i. The corresponding eigenvectors also looked completely different than the results shown in the tutorial file. I experienced no such problems, however, when I ran the stability analysis with the "MultipleModes" option. Could there be an issue with the "SingleMode" option on multiple processors? I would be very grateful for your assistance. Best regards, Cheng

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doxygen documentation TimeIntegrationScheme
by Martin Wilfried Hess 17 May '21

17 May '21

******************* 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, I am using the current master branch to implement time-dependent model reduction for incompressible CFD. The current doxygen documentation has deviated significantly from the code. For example I cannot reconstruct what happened to Nektar::LibUtilities::TimeIntegrationScheme Class Reference as documented here https://doc.nektar.info/doxygen/latest/class_nektar_1_1_lib_utilities_1_1_t… Martin -- -- Martin Hess, Ph.D., Post-doctoral research fellow SISSA mathLab, International School for Advanced Studies Office A-434 (4th floor), via Bonomea 265, I-34136 Trieste, Italy phone: +39 040 3787 491 email: mhess(a)sissa.it

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Element-specific filter architecture
by Vidhi Zala 14 May '21

14 May '21

******************* 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, I am working on adding a filter in accordance with the SolverUtils/Filter architecture. It performs element-type specific operations. Instead of creating a monolithic filter that checks for the element type and performs operations, I want to break it down into subfilters. Should these go into StdRegions/ since they are element-specific or stay in SolverUtils? It will help if someone can point to an example scenario of an existing filter designed this way. Thanks, V ,-~~-.___._. / | ' \ | |--------. Vidhi Zala ( ) 0 | | | School of Computing \_/-, ,----' | | | Scientific Computing and Imaging Institute ==== !_!-v---v--. University of Utah / \-'~; .--------. / __/~| ._-""|| | vidhi.zala(a)utah.edu =( _____|_|____||________| http://sci.utah.edu/people/vidhi.html I support Ruff Haven Crises Shelter for Homeless Pets <https://www.ruffhaven.org/donate>. Consider a donation today :)

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Error "gen_bndry: Illegal B.C. function definition" in Hidden Fluid Mechanics platform.
by Jean Schuster 10 May '21

10 May '21

******************* 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 everybody. I hope everybody is doing good. My name is Jean Schuster, from Brazil. I'm starting my studies in neural networks and machine learning, when I found a subject of interest in a paper named Hidden fluid mechanics: Learning velocity and pressure fields from flow visualizations <https://science.sciencemag.org/content/367/6481/1026>. In that papar, Dr. Raissi, Dr. Yazdani and Dr. Karniadakis addressed a fluid mechanics problem of flow visualization, like smoke or dye visualization for qualitative characterization of flow fields, "injecting" a passive escalar (say smoke) through a transport equation together with the Navier-Stokes equations, developing a framework that they called hidden fluid mechanics (HFM), a physics-informed deep-learning framework capable of encoding the Navier-Stokes equations into the neural networks while being agnostic to the geometry or the initial and boundary conditions. That framework uses Nektar, that I suppose they had modified to insert the passive scalar transport equation, to run the CFD simulations for the example problems they demonstrate in the papar. It can be downloaded under a GNU general public license at: https://github.com/alirezayazdani1/HFM After some days I managed to compile it and its dependencies in a 64bits Ubuntu 20.04.2 LTS machine. I attached a file called log_compiling.txt that contains the terminal output during the compiling process. Everything seems fine, but when I try to run, for example the classic problem of a flow over a cylinder that is included in the framework, I get an error saying: gen_bndry: Illegal B.C. function definition. I'm using the following command to run the example: ./nektar -V -chk -S -n4 ./RUN/Cylinder2D/cylinder2d.rea 2>&1 | tee log_run_cyl2d.txt It returns: jean@Prandtl:~/HFM/SourceCode$ ./nektar -V -chk -S -n4 ./RUN/Cylinder2D/cylinder2d.rea 2>&1 | tee log_run_cyl2d.txt rcm bandwidth (u) : 18080 [204031 (0)] Input File : /RUN/Cylinder2D/cylinder2d Concat files : 0 Re (U=1, L=1) : 100 Time step : 0.0008 Integration order : 2 Number of modes : 4 Number of elements : 45856 Number of Families : 45856 Equation type : Navier-Stokes (convective) Integration time : 120.008, or 150010 steps I/O time for saves : 40, or 50000 steps [checkpoint] NS Scheme Type : Splitting scheme Solver Type : Direct RCM gen_bndry: Illegal B.C. function definition Follow attached the cylinder2d.rea file. I would try to use some of the tutorials available here https://www.nektar.info/community/tutorials/ with the compiled code, but it returns me an error saying "The requested URL was not found on this server" in every link in the tutorials page. I'm pretty sure that this is not exactly the right place for this question, but I don't know where else I could get help. So I hope I'm not bothering any of you. Thanks in advance. Best regards, Jean.

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Parallel 3DH2D simulation
by Xiao, Chengnian 09 May '21

09 May '21

******************* 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, I would like to know if the latest nektar++ version supports parallel 3DH2D simulation, i.e. 3D configuration based on 1D mesh and Fourier expansions in y,z directions? According to the user-guide, there are ---npz, -npy,--npx options available. However, whenever I run the 3DH2D test case provided in the sample session file ChanFlow_3DH2D_FFT.xml on multiple processors with mpirun -np >1, the solver would crash after initialization, no matter if npx, npy or npz are specified to be greater than 1 or not. The case does work fine however on a single processor. Best regards, Cheng

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Apply filer to a specified domain range
by Stanisław Gepner 03 May '21

03 May '21

******************* 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, I was wandering if it is possible to program into a Filter a possibility to be applied onto a selected range of the domain. Much like what is possible using FieldConvert -r option. I looked at the code, and there is the DomainRange, but I am not sure there is a way to use it on ExpList through which I access coordinates, physical values from within the Filter. One solution I see is to just go through what is available through GetCoords() (at initialization) and create a mask to filter out values from outside the specified range. The filter I am working on is based on quantities integrated from the fields, So I think I could create the mask at initialization and than use it at updates to zero-out values outside. But might it be, that something like this is already implemented? Any suggestions are welcome. Cheers! Stan -- Best regards, Stanisław Gepner, Ph.D. *Faculty of Power and Aeronautical Engineering* Nowowiejska 21/25 Str. 00-665 Warsaw, Poland phone +48 (22) 234 51 70 <https://www.pw.edu.pl/engpw>

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Post-processing - Wall Shear Stress
by Paulo henrique Ferreira 03 May '21

03 May '21

******************* 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, I ran a typical simulation of a circular cylinder at Re = 3900, but now I'm having to deal with a small issue in the post-processing. I'm unable to properly obtain the wall shear stress, some ripples appear along the span, as shown in the screenshot. The C0 projection (FieldConvert module) has not worked and I'm not sure if it should have worked to the surface mesh obtained from the XML file. Does anyone know what I should do to fix this problem or have any other suggestions in this case? Thank you! Regards, Paulo Henrique PhD StudentInstituto Tecnologico de Aeronautica - ITA 12228-900 - Sao Jose dos Campos - SP - BRAZIL

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