- Nektar-users - imperial.ac.uk

Compilation problems - macOS Mojave
by Denny, Ryan 06 Dec '18

06 Dec '18

Hi all, Has anyone had issues with compilation since upgrading to Mojave? I’ve updated all required packages but get the attached error message, which appears when the compiler tries to link the LibUtilities library. Thanks, Ryan

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Hi all question about Possible choices for the expansion TYPE for mesh cells
by Moto Light 30 Nov '18

30 Nov '18

Hi all, i need to know what is the different between the three types in order to expansion my mesh cells Modal MODIFIED Nodal GLL_LAGRANGE Nodal SEM GLL_LAGRANGE_SEM Thanks, Regards.

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File naming convention for APESolver
by Amitvikram Dutta 27 Nov '18

27 Nov '18

Hello everyone, I'm trying to use the APESolver using a time-dependent series of files for my baseflow and my source terms. I'm having difficulty in figuring out the regex that's used to specify the format of these file names. From the tutorial the file names are specified in the .xml file as thus: APEzzz_%14.8E.pts while the actual filename this points to is : APEzzz_1.00000000E-05.pts and so on. I can't quite decipher the regex. Observation tells me that the 14 refers to the total number of characters after the underscore and 8 is the number of zeros between the decimal point and the E. However, since my input .pts file come directly from a simulation it would be easier for me if I could provide the regex to the .xml file to access filenames of the form APEzzz_1401.pts, APEzzz_1402.pts and so on. I have tried APEzzzz_%4.pts as an input but this returns an error. I'd be grateful for some further guidance in this regard. Sincerely, -- *Amitvikram Dutta* Graduate Research Assistant Fluid Mechanics Research Lab Multi-Physics Interaction Lab University of Waterloo

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Handling Pyramids
by Vishal Saini 26 Nov '18

26 Nov '18

Hi all, I've imported a mesh from gmsh that contains a layer of *pyramids* for transitioning between hexes and tets using: *NekMesh JICF_NektP2_2comp.msh JICF_NektP2_2comp.xml* Output: *Multiple elements in composite detected; remapped:- Tag 1 => 11 (Tetrahedron), 10 (Pyramid), 1 (Hexahedron)* No problem on NekMesh level. Defining my expansion as: *<E COMPOSITE="C[1,10,11]" NUMMODES="3" FIELDS="u,v,w,p" TYPE="MODIFIED" />* when I run (Nektar++ v 4.4.1) using: *mpirun -npernode 28 -np 56 IncNavierStokesSolver -v JICF_NektP2_2comp_xml conditions_JICF_2D.xml* (using prepartitioned mesh). I get the following "note": *Collection Implemenation for Tetrahedron ( 3 3 3 ) for ngeoms = 24960Note: Implementation does not exist: Pyramid, BwdTrans, SumFac, ModalNote: Implementation does not exist: Pyramid, IProductWRTBase, SumFac, ModalNote: Implementation does not exist: Pyramid, IProductWRTDerivBase, SumFac, ModalNote: Implementation does not exist: Pyramid, PhysDeriv, SumFac, ModalNote: Implementation does not exist: Pyramid, BwdTrans, SumFac, ModalNote: Implementation does not exist: Pyramid, IProductWRTBase, SumFac, ModalNote: Implementation does not exist: Pyramid, IProductWRTDerivBase, SumFac, ModalNote: Implementation does not exist: Pyramid, PhysDeriv, SumFac, Modal* What does it mean? How can I fix it? Do Pyramids need to be treated in a somewhat different way? BR, Vishal --- *Vishal SAINI*

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Re: [Nektar-users] Regarding reconstruction 3D eigenmode from biGlobal linear stability with HalfMode
by Abhishek Kumar 20 Nov '18

20 Nov '18

Dear Spencer and David, Thanks for your response. 1) Yes, I am running a passive scalar using a forcing term to couple the scalar. The code was working well for 2D base flow and 2D perturbation, but there was an issue with the HalfMode calculation. Now, this is resolved as there was a bug in “LinearisedAdvection::UpdateGradBase”. It was not including the passive scalar because of condition “if var<2” for "HalfMode". Now, when I change it to “if var < 4”, it works. 2) David: I tried your suggestion, but it doesn't work. I think we need a module to perform inverse Fourier transform in the homogeneous direction of the eigenmode obtain from the HalfMode calculation. Again thanks a lot to both for your help. With regards Abhishek On Tue, Nov 20, 2018 at 1:58 PM Moxey, David <D.Moxey(a)exeter.ac.uk> wrote: > Hi both, > > This might be possible without doing anything fancy, unless I am > forgetting how the half mode output looks like. Have you tried just doing: > > FieldConvert session.xml halfmode.fld out.vtu > > where session.xml has been set up as a 3DH1D problem? This might then just > populate the mean mode and zero the rest of the spectrum so you will get > the mean mode output. > > Cheers, > > Dave > > > On 20 Nov 2018, at 13:24, Sherwin, Spencer J <s.sherwin(a)imperial.ac.uk> > wrote: > > > > Dear Abhishek, > > > > I have just been trying to catch up on your thread with Stan. Do I > understand you have the stability now running correctly with a passive > scalar using a forcing term to couple the scalar? > > > > If I next understand your question you want to plot the output from a > half mode eigenfield as a 3D image? This certainly used to be possible > although I have not played with this bit of code for a while. Essentially > we need to add a mean mode component to the eigenmode to make it a full > 3D1H expansion and then FieldConvert should work. > > > > I will try and have a dig around and see what might allow you to do this > since I cannot see anything in the user-guide. > > > > Cheers, > > Spencer. > > > >> On 10 Nov 2018, at 07:43, Abhishek Kumar <abhishek.kir(a)gmail.com> > wrote: > >> > >> > >> Hi friends, > >> > >> I think I have not explained my problem properly in my last email. > >> > >> Actually, I am doing biGlobal linear stability analysis with HalfMode, > which yields eigenmode on a 2D plane. Now I want to reconstruct the > eigenmode in 3D, which will require inverse Fourier transform. I have > check one of the examples in the manual for the Floquet analysis of a of > flow past a cylinder. There is a plot for the eigenmode at z=2 [Figure > 10.25 of the manual]. > >> > >> Thus, I want to know which module is used to convert the eigenmode in > 3D. > >> > >> I would be highly thankful for the comments on this issue. > >> > >> > >> With regards > >> Abhishek Kumar > >> > >> > --------------------------------------------------------------------------------------- > >> Abhishek Kumar > >> Research Associate > >> Applied Mathematics Research Centre > >> Coventry University, Coventry CV1 5FB > >> The United Kingdom > >> > >> Email # ac7600(a)coventry.ac.uk, abhishek.kir(a)gmail.com > >> > --------------------------------------------------------------------------------------- > >> _______________________________________________ > >> Nektar-users mailing list > >> Nektar-users(a)imperial.ac.uk > >> https://mailman.ic.ac.uk/mailman/listinfo/nektar-users > > > > Spencer Sherwin FREng, FRAeS > > Head, Aerodynamics, > > Director of Research Computing Service, > > Professor of Computational Fluid Mechanics, > > Department of Aeronautics, > > s.sherwin(a)imperial.ac.uk South > Kensington Campus, > > Phone: +44 (0)20 7594 5052 Imperial College > London, > > Fax: +44 (0)20 7594 1974 London, SW7 > 2AZ, UK > > http://www.imperial.ac.uk/people/s.sherwin/ > > > > _______________________________________________ > > Nektar-users mailing list > > Nektar-users(a)imperial.ac.uk > > https://mailman.ic.ac.uk/mailman/listinfo/nektar-users > > -- With regards Abhishek Kumar --------------------------------------------------------------------------------------- Abhishek Kumar Research Associate Applied Mathematics Research Centre Coventry University, Coventry CV1 5FB The United Kingdom Email # ac7600(a)coventry.ac.uk, abhishek.kir(a)gmail.com ---------------------------------------------------------------------------------------

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Regarding reconstruction 3D eigenmode from biGlobal linear stability with HalfMode
by Abhishek Kumar 20 Nov '18

20 Nov '18

Hi friends, I think I have not explained my problem properly in my last email. Actually, I am doing biGlobal linear stability analysis with HalfMode, which yields eigenmode on a 2D plane. Now I want to reconstruct the eigenmode in 3D, which will require inverse Fourier transform. I have check one of the examples in the manual for the Floquet analysis of a of flow past a cylinder. There is a plot for the eigenmode at z=2 [Figure 10.25 of the manual]. Thus, I want to know which module is used to convert the eigenmode in 3D. I would be highly thankful for the comments on this issue. With regards Abhishek Kumar --------------------------------------------------------------------------------------- Abhishek Kumar Research Associate Applied Mathematics Research Centre Coventry University, Coventry CV1 5FB The United Kingdom Email # ac7600(a)coventry.ac.uk, abhishek.kir(a)gmail.com ---------------------------------------------------------------------------------------

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the bug in analytical expressions evaluation
by A.P. 19 Nov '18

19 Nov '18

Hello, I calculated a boundary condition <D VAR="u" VALUE="-y^2+1.0" /> and had found that the expression "-y^2+1.0" had calculated as "(-y)^2+1.0". The "1-y^2" and the "-(y^2)+1.0" are OK. Alexander.

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Regarding three-dimensional eigenmode
by Abhishek Kumar 09 Nov '18

09 Nov '18

Hi, I am doing biGlobal linear stability analysis with HalfMode. I want to convert the 2D eigenmode to the real space in 3D. Is there any utility to convert the eigenmode? With regards Abhishek Kumar --------------------------------------------------------------------------------------- Abhishek Kumar Research Associate Applied Mathematics Research Centre Coventry University, Coventry CV1 5FB The United Kingdom Email # ac7600(a)coventry.ac.uk, abhishek.kir(a)gmail.com ---------------------------------------------------------------------------------------

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Mapping Variables from Different Solvers
by Khaled Younes 09 Nov '18

09 Nov '18

Hello, I am trying to map variables from the CompressibleFlowSolver to the baseflow in APESolver for a coupled simulation that I am running. I was successfully able to map the pressure and density using: ‘<F VAR="p0" FILE="File.fld:p" />’ ‘<F VAR="rho0" FILE="File.fld:rho" />’ However, the same syntax does not apply for the velocity field, as the CompressibleFlowSolver solves for the momentum directly: ‘rhou, rhov’. Is there a way I can convert these variables to ‘u,v’ by dividing by the density? Thanks, Khaled Younes

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Re: [Nektar-users] FW: Nektar++ installation in a cluster
by Amitvikram Dutta 05 Nov '18

05 Nov '18

Hi Nitish, Did you turn off the BUILD_THIRDPARTY options on the ccmake screen? I had a similar problem. I placed a ThirdParty folder containing the tarballs of all the thirdparty dependencies in the NEKTAR_SRC directory (which contains the build dir) and turned off the options that I mentioned above. That worked for me. Sincerely, On Tue, Oct 30, 2018 at 9:23 AM Amitvikram Dutta < amitvikram.dutta(a)uwaterloo.ca> wrote: > > ------------------------------ > *From:* nektar-users-bounces(a)imperial.ac.ukOn Behalf OfNitish Arya > *Sent:* October 30, 2018 8:21:04 AM (UTC-05:00) Eastern Time (US & Canada) > *To:* nektar-users(a)imperial.ac.uk > *Subject:* [Nektar-users] Nektar++ installation in a cluster > > Hello. > > I am planning to use APE solver included in the nektar framework. I have > to configure the MPI using Intel MPI which is available in the cluster, > while dependencies are installed using an internet connection. The internet > connection is only available at the head node in which I am unable to > invoke the Intel MPI. So it means that I have to compile the dependencies > separately. I tried compiling the ThirdParty dependencies separately but > when I compiled Nektar, it was again searching for the dependencies via > http or https ( both of the protocols are also not working ). > > Is there any way I can install Nektar without the installer searching for > the dependencies in the internet. > > > Sincerely, > Nitish > -- *Amitvikram Dutta* Graduate Research Assistant Fluid Mechanics Research Lab Multi-Physics Interaction Lab University of Waterloo

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