June 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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Can Nektar++ filter architecture work for my filter application?
by Vidhi Zala 15 Jul '21

15 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 implementing an algorithm that takes an intermediate solution [image: {U}_n] at time n and transforms it to [image: \tilde{U}_n]. Inside SolverUtils/UnsteadySystem.cpp, I want to feed this transformed value back to the TimeIntegrate() call at the beginning of the time loop, so [image: {U}_{(n+1)}] will be formed using [image: \tilde{U}_n]. I wrote a Nektar++ filter that takes the m_fields object and modifies its phys and coeffs attributes using my filter's update() method. Upon return, I verify that m_fields indeed have [image: \tilde{U}] , which are different from the [image: U]. But the change is not passed to the next integration timestep. I tried to update the local variable "fields" used to initialize the integration scheme from [image: {U}_n] to [image: \tilde{U}_n]. The integration object is still unaware of the change to the intermediate solution. I suspect that the time integration object does not expose a *setter *method for the solution vector objects. I checked all the existing Nektar++ filters, but from my understanding, none of those change the values of the intermediate solutions. The only way I could get my filter to work is by calling the initializer of the time integration scheme at every timestep with the modified "fields" object. While it works for my experiments, I need advice about where architecture-wise, should I put my *filter *such that I don't need to modify UnsteadySystem.cpp at all. Thanks much! 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

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Regarding online Nektar++ workshop
by Abhishek Kumar 12 Jul '21

12 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. ******************* Hello all, I hope everyone is doing well. I wanted to suggest about Nektar++ workshop. Unfortunately, due to COVID, this workshop was postponed. Still, it looks that it will be hard to organise a regular workshop. Will it be possible to organise an online Nektar++ workshop this year. With regards Abhishek -- --------------------------------------------------------------------------------------- Abhishek Kumar Assistant Professor (Research) Centre for Fluid and Complex Systems Coventry University, Coventry CV15FB The United Kingdom Phone: +44 24 7765 9150 Mobile: +44 7464026494 ---------------------------------------------------------------------------------------

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why is PhysDeriv not a linear function
by Martin Wilfried Hess 24 Jun '21

24 Jun '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. ******************* Hello, I am calling PhysDeriv from an Expansion Class Object. Why is this not linear? In the sense that if I call PhysDeriv for any linear combination of vectors it should be the same as computing the linear combination of the PhysDeriv of the vectors. Martin Hess -- -- 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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Fix for addfld module
by Abhishek Kumar 21 Jun '21

21 Jun '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 detected a bug with addfld module of FieldConvert in master branch. This error is coming as the expansion is not initialised. It works if we add m_f->SetUpExp(vm); at the beginning of "ProcessAddFld::Process(po::variables_map &vm) " function, and also remove "boost::ignore_unused(vm);". I hope this can be corrected in the master branch. With regards Abhishek -- --------------------------------------------------------------------------------------- Abhishek Kumar Assistant Professor (Research) Centre for Fluid and Complex Systems Coventry University, Coventry CV15FB The United Kingdom ---------------------------------------------------------------------------------------

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Aerodynamic forces
by Alessandro Alberto de Lima 18 Jun '21

18 Jun '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 Guys, I would like to know how the aerodynamic forces are calculated in nektar, the dimensions of the values on the .fce output file and its relation with the aerodynamic coefficients. Thank you. Alessandro

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Boundary layer mesh
by Ezat Shokrani 12 Jun '21

12 Jun '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 working on numerical simulation of blood flow in arteries. The flow regime of my case study is laminar. In addition to obtaining velocity and pressure field, the evaluation of shear rate and WSS for this case is also important for me. Therefore, in addition to using tetrahedral elements as core mesh, I am going to employ prism layers for resolving the boundary layer next to the wall. I have seen, in the literature, that there are two approaches for producing the boundary layer mesh that most groups use them. Firstly, some groups consider a constant total thickness for boundary layer mesh. This means that during the mesh study process, they do not change the overall thickness but they try to increase the number of layers. Secondly, other groups consider a constant number of layers for the boundary layer mesh (e.g. three layers for the coarse mesh) during the mesh study and when they refine the mesh in each step, the element size of each layer decreases. As a result, the total thickness of boundary layer mesh decreases too. Meanwhile, I have encountered some questions related to these approaches for producing boundary layer mesh. I have seen in articles related to the blood flow simulation which is done using Nektar++, p-refinement method has been used for mesh study process which I think this mimics the first approach. My question is that how I can calculate the total thickness of the boundary layer mesh (both steady and pulsatile flow conditions) through the mesh study. Related to the second approach, I have seen different research teams have various opinions for constructing the boundary layer mesh even for the cases with similar geometry and flow conditions. For example, different groups produce boundary layer mesh with a range of 3 to 20 layers. In addition, some consider a constant thickness for “each” layer (with no growth factor). However, others try to use a growth factor to vary the thickness of each layer. Even, different groups use a variety of core element size to boundary layer size ratio to construct the mesh. I know that this depends on the case study but they did not mention any reason for their choices. I would like to know whether or not there is a rule of thumb for this process or if there is a good guess for producing the boundary layer mesh with respect to this approach. I would be wondering if you could guide me on these issues. Best regards, Ezat Shokrani,

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NekMesh statistics per element type
by Vidhi Zala 12 Jun '21

12 Jun '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 able to get some statistics while generating XML from msh using the verbose mode of NekMesh. However, it provides information in aggregate 2D and 3D elements. I wonder if there is a method to query NekMesh that provides details on the distribution of 2D and 3D elements? 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

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Problem to install Nektar++ 5.0.1 in macOS Catalina 10.15.7
by Eduardo Lopez Bravo 09 Jun '21

09 Jun '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. ******************* Hello Nektar team, I'm brand new on Nektar++ community. I've been trying to install Nektar++ on my macOS Catalina 10.15.7 but nothing seems to work. I've taken a screenshot of the error message while I tried to configure Nektar dependencies following the user manual. I have installed the seven packages required using Homebrew, and additionally I have installed some other packages (METIS, FFTW, Open Cascade CE, Tetgen and Triangle). Not only that, but I've been trying to install the latest version of Nektar on my macOS, but I haven't succeeded. That's the main reason I have tried it with the 5.0.1 version. If someone has succeeded at installing Nektar++ in this macOS version, could you please tell me what you did so it can work? Any help will be extremely appreciated! Kind regards, Eduardo. PD: I suspected there is a problem among CMAKE Version 3.20.3 and BLAS/LAPACK packages. [image: Error message Nektar.png]

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Some problems with post-processing FieldConvert
by gongminjiang＠hrbeu.edu.cn 08 Jun '21

08 Jun '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. ******************* Hello! I want to generate Q-criterion and vorticity isocontour in Tecplot, and also I use C0Projeciton to smooth data, but the visualization quality is not good. Do I still have some skills to make the isocontour smooth? Best wishes!

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