January 2020 - Nektar-users

Element with max CFL
by Vishal Saini 02 Apr '20

02 Apr '20

Hi all, Quick question: Has anyone tried to check the location of a particular element in the mesh? A log file reports the maximum (?) CFL and the corresponding element as: "CFL: 0.0337915 (in elmt 94488)"? Is there a quick way to locate "elmt 94488"? Cheers, Vishal

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Manipulate 3DH1 chk/fld file in Fourier space
by F Mellibovsky 16 Mar '20

16 Mar '20

Dear all, I have run a 3DH1 simulation and I need to set all Fourier coefficients to zero except those corresponding to a fundamental wavelength and its harmonics (e.g. keep only modes 0, +-5, +-10, etc and set all the rest to zero). I have the intuition that some combination of FieldConvert options can accomplish exactly this, but I am unsure of what is the best (or some) way to proceed. My guess is that the "homplane:wavespace:planeid=?" can be used to extract the individual Fourier modes, but I am unsure as to how the Fourier modes are sorted and which ones must be extracted to recover a chosen fundamental wavelength and its harmonics (both real and imaginary parts, or modulus and argument, or however the Fourier modes are stored). The only one I'm pretty sure of is mode 0 or mean mode. Once I get the individual fld files for each one of the modes, I was intending to use the "addfld:fromfld=mode1.fld:scale=1 mode1.xml mode2.fld newfile.fld" sequentially to build a solution from the chosen modes. The issue here is that the fields extracted with "homplane" seem to be 2D and would therefore need to be recast in 3DH1 form before proceeding to "addfld". How can this be done? Thanks in advance for your help Fer Mellibovksy

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error MSB6006: "cmd.exe" exited with code 1
by Silvia Ceccacci (HDR) 23 Jan '20

23 Jan '20

******************* This email from 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 am Silvia Ceccacci, from Macquarie University. I am trying to install Nextar on Windows but I am having some troubles with it. Here my questions: 1) Is MS Visual Studio 2019 working for Nektar? I can see the 2015 is preferred and I have tried to use it but it gave me some issues. The 2019 version seems to work fine when I generate the build scripts with CMake. 2) When I issue the command: msbuild INSTALL.vcxproj /p:Configuration=Release on the Visual Studio 2019 terminal, I get this error: error MSB6006: "cmd.exe" exited with code 1 Could you please help me understand what I should be doing and how to solve this problem? Thank you. Kind regards Silvia

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Up-to-date build from source on IC HPC cluster
by Thibaut Appel 20 Jan '20

20 Jan '20

Hello, I was just wondering how people compile Nektar++ from source on the IC cluster these days and if there are any recommended adjustments compared with that this link says https://www.nektar.info/nektar-cx1/ It is 4 years old but the instructions still work, it seems I'm able to compile Nektar++ with module load mpi/intel-2019.6.166 module load intel-suite/2017.6 module load fftw/3.3.3-double module load flex/2.6.4 module load scotch/6.0.4 module load boost/1.66.0 CC=mpicc CXX=mpicxx cmake -DNEKTAR_USE_FFTW=ON -DNEKTAR_USE_MKL=ON DNEKTAR_USE_MPI=ON -DNEKTAR_USE_SYSTEM_BLAS_LAPACK=OFF -DNEKTAR_TEST_FORCEMPIEXEC=ON -DCMAKE_CXX_FLAGS="-std=c++11 -O3 -xSSE4.2 -axAVX,CORE-AVX-I,CORE-AVX2" -DCMAKE_C_FLAGS="-O3 -xSSE4.2 -axAVX,CORE-AVX-I,CORE-AVX2" .. Would you recommend any change with respect to newer packages or better practice for efficiency? Thanks for the support, Thibaut

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Re: [Nektar-users] Aeroacoustics using cwipi in nektar++-5
by Kilian Lackhove 15 Jan '20

15 Jan '20

******************* This email from 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 Nitish, Great to hear it works for you, i will add the note to the userguide then. Regarding the implementation: The Coupling writes its received data directly into the m_Forcing array. Unfortunately, the Upate method in ForcingBody.cpp would allocate a new array each time step. By using FIELDFORCETIMEFCN, the m_hasTimeFcnScaling flag is set to true and Update is called only once during initialization (which is fine), so the arrays stay the same. The condition with the "x y z t" does not check the expression of the CouplingSource function, but its variables, which are set elsewhere in the code and cannot be altered by the user IIRC. So that has nothing to do with the Coupling. Cheers, Kilian Am 14.01.20 um 07:03 schrieb Nitish Arya: > Dear Kilian, > > I looked into the code and found that when no value is provided to an > expression, it adds "x y z t" to it. In the ForcingBody.cpp the > coupling force is read if there is no value (or the other way round, I > am still confused) provided for the CouplingSource function. But the > following worked for me. > > <FUNCTION NAME="CouplingSource"> > <E VAR="p,u,v,w" VALUE =" "/> > </FUNCTION> > </CONDITIONS> > <FORCING> > <FORCE TYPE="Field"> > <FIELDFORCE> CouplingSource <FIELDFORCE/> > <FIELDFORCETIMEFCN> 1.0 </FIELDFORCETIMEFCN> > </FORCE> > </FORCING> > > I am able to read the source terms as well as the base fields now. > > regards, > Nitish > > > On Tue, 14 Jan, 2020, 1:24 AM Kilian Lackhove, <kilian(a)lackhove.de > <mailto:kilian@lackhove.de>> wrote: > > Hi Nitish, > > i am glad to hear you got the setup working. Regarding the > forcing, you > need to set > > <FIELDFORCETIMEFCN> 1.0 </FIELDFORCETIMEFCN> > > (see e.g. solvers/DummySolver/Tests/Dummy_3DCubeCwipi_0.xml for an > example) > > This is a workaround for an incompatibility between the way the > forcing > is implemented and how the coupling works. Let me know if it > worked for > you so i can add this piece if info to the userguide. > > Cheers, > > Kilian > > > Am 09.01.20 um 16:16 schrieb Nitish Arya: > > Dear Kilian, > > > > Thank you very much for your suggestion. The cwipi functionality in > > the new release really solved my problem. I also successfully > compiled > > the openfoam interface [3] with the acoustic solver in nektar. The > > reception of base fields (u0,v0,w0) is absolutely fine. However, > when > > I tried receiving the source terms (F_0_p, F_0_u, F_0_v, F_0_w), > the > > corresponding fields are not reflected in nektar. The source > terms are > > zero everywhere (since they were initialized to zero in the > > configuration file). This could mean that after the transfer > they are > > being modified to the value in the configuration file. Am I missing > > something? > > > > I have also attached the conditions file in the mail. > > > > > > > > regards, > > Nitish > > > > >

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Problem to solve the Forward Step test
by Victoria Korchagova 14 Jan '20

14 Jan '20

******************* This email from 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 want to use Nektar++ Compressible Flow Solver for modelling of supersonic flows and testing of different techniques of the shock-capturing in future. I have tried to run a simple test Forward Step (Woodward, Collela) by CompressibleFlowSolver, but some problems have appeared. The simulation is stable only for CFL = 0.001. Increasing of CFL causes a vacuum on the first step. My mesh resolution is 8 cells per step height. My settings: <EXPANSIONS> <E COMPOSITE="C[5]" NUMMODES="3" FIELDS="rho,rhou,rhov,E" TYPE="MODIFIED" /> </EXPANSIONS> <CONDITIONS> <PARAMETERS> TimeStep = 0 CFL = 0.001 FinTime = 4.0 NumSteps = 0 IO_CheckSteps = 1000 IO_InfoSteps = 500 Gamma = 1.4 rhoInf = 1.0 uInf = 3.0 vInf = 0.0 pInf = 1.0 / Gamma mu = 1e-12 cInf = sqrt(Gamma * pInf / rhoInf)  Skappa = -1.3 Kappa = 0.2 mu0 = 1.0 </PARAMETERS> <SOLVERINFO> </SOLVERINFO> <VARIABLES> <V ID="0"> rho </V> <V ID="1"> rhou </V> <V ID="2"> rhov </V> <V ID="3"> E </V>  </VARIABLES> <BOUNDARYREGIONS> C[1] C[2] C[3] C[4] </BOUNDARYREGIONS> <BOUNDARYCONDITIONS> <REGION REF="0"> <D VAR="rho" VALUE="rhoInf" /> <D VAR="rhou" VALUE="rhoInf*uInf" /> <D VAR="rhov" VALUE="0" /> <D VAR="E" VALUE="pInf / (Gamma - 1) + 0.5 * rhoInf * (uInf * uInf + vInf * vInf)" />  </REGION> <REGION REF="1"> <D VAR="rho" USERDEFINEDTYPE="PressureOutflowNonReflective" VALUE="rhoInf" /> <D VAR="rhou" USERDEFINEDTYPE="PressureOutflowNonReflective" VALUE="rhoInf*uInf" /> <D VAR="rhov" USERDEFINEDTYPE="PressureOutflowNonReflective" VALUE="0" /> <D VAR="E" USERDEFINEDTYPE="PressureOutflowNonReflective" VALUE="pInf / (Gamma - 1) + 0.5 * rhoInf * (uInf * uInf + vInf * vInf)" />  </REGION> <REGION REF="2"> <D VAR="rho" USERDEFINEDTYPE="Wall" VALUE="0" /> <D VAR="rhou" USERDEFINEDTYPE="Wall" VALUE="0" /> <D VAR="rhov" USERDEFINEDTYPE="Wall" VALUE="0" /> <D VAR="E" USERDEFINEDTYPE="Wall" VALUE="0" />  </REGION> <REGION REF="3"> <D VAR="rho" USERDEFINEDTYPE="Wall" VALUE="0" /> <D VAR="rhou" USERDEFINEDTYPE="Wall" VALUE="0" /> <D VAR="rhov" USERDEFINEDTYPE="Wall" VALUE="0" /> <D VAR="E" USERDEFINEDTYPE="Wall" VALUE="0" />  </REGION> </BOUNDARYCONDITIONS> <FUNCTION NAME="InitialConditions"> <E VAR="rho" VALUE="rhoInf" /> <E VAR="rhou" VALUE="rhoInf * uInf" /> <E VAR="rhov" VALUE="rhoInf * vInf" /> <E VAR="E" VALUE="pInf / (Gamma - 1) + 0.5 * rhoInf * (uInf * uInf + vInf * vInf)" />  </FUNCTION> </CONDITIONS> I’ll be very thankful for help! -- Best regards, Victoria Korchagva

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Re: [Nektar-users] Aeroacoustics using cwipi in nektar++-5
by Kilian Lackhove 13 Jan '20

13 Jan '20

******************* This email from 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 Nitish, i am glad to hear you got the setup working. Regarding the forcing, you need to set <FIELDFORCETIMEFCN> 1.0 </FIELDFORCETIMEFCN> (see e.g. solvers/DummySolver/Tests/Dummy_3DCubeCwipi_0.xml for an example) This is a workaround for an incompatibility between the way the forcing is implemented and how the coupling works. Let me know if it worked for you so i can add this piece if info to the userguide. Cheers, Kilian Am 09.01.20 um 16:16 schrieb Nitish Arya: > Dear Kilian, > > Thank you very much for your suggestion. The cwipi functionality in > the new release really solved my problem. I also successfully compiled > the openfoam interface [3] with the acoustic solver in nektar. The > reception of base fields (u0,v0,w0) is absolutely fine. However, when > I tried receiving the source terms (F_0_p, F_0_u, F_0_v, F_0_w), the > corresponding fields are not reflected in nektar. The source terms are > zero everywhere (since they were initialized to zero in the > configuration file). This could mean that after the transfer they are > being modified to the value in the configuration file. Am I missing > something? > > I have also attached the conditions file in the mail. > > > > regards, > Nitish > >

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Regarding our paper in JFM
by Abhishek Kumar 13 Jan '20

13 Jan '20

******************* This email from 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 friends, I am happy tell that our paper titled "Mixed baroclinic convection in a cavity" is now published in JFM. We have extensively used incompressible solver with a buoyant scalar of Nektar++. I have attached a copy of the paper in this email. I would like to thank the entire team of Nektar++ for the support during this work and giving me an opportunity to present this result during the last Nekar++ workshop. With regards Abhishek -- --------------------------------------------------------------------------------------- Abhishek Kumar Research Associate Centre for Fluid and Complex Systems Coventry University, Coventry CV15FB United Kingdom Webpage: https://abhishekkir.wixsite.com/website Email # ac7600(a)coventry.ac.uk, abhishek.kir(a)gmail.com Phone: +44 24 7765 9150 Mobile: +44 7464026494 ---------------------------------------------------------------------------------------

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r-adaptation
by 蒋树杰 05 Jan '20

05 Jan '20

******************* This email from 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, Now I want to use Nektar++ to do some transonic simulation (Compressible Solver). I want to increase the resolution for shocks. I find a PDF named 'Mesh adaptation (r & p) for compressible flows in Nektar++', given by Joaquim Peiro et al. They mentioned r-adaptation can be used by clustering nodes near shocks. But I can not find more information about this. Is this function available in Nektar++ 5.0.0? If someone is familiar with this, please let me know. Merry Christmas! Thank you for your help! Shujie University of Southampton

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Field Interpolation during runtime
by Nitish Arya 05 Jan '20

05 Jan '20

******************* This email from 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 perform an aeroacoustic simulation in which I am using APESolver (nektar-4.4.1). I am transferring the source terms from the fluid solver (OpenFoam) to nektar++. I need to interpolate the source terms from the finite volume mesh (which is relatively coarser) ino the spectral mesh which can be used by APESolver. Initially, I used Shepard's algorithm to interpolate the source terms which performed well for serial runs but, unfortunately, there are several numerical errors when I am passing the data using multiple processors. Recently I found out that there is an already available utility in nektar++ for field interpolation ( as post-processing utility). I wanted to inquire if it is possible to use the functionality for interpolating the data during runtime with multiple processors. Happy new Year to all of you!! regards, Nitish Arya Department of Aerospace Engineering IIT Kanpur, India

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