- Nektar-users - imperial.ac.uk

Bug in LDG
by Aidyn Aitzhan 19 Jun '19

19 Jun '19

Dear all, Whenever I use 2 or more equations with different types of boundary conditions for diffusion, convection-diffusion with LDG I obtain something weird. For example, a solution obtained using the attached file is just random noise. However, when I run problems separately or use implicit diffusion advancement (discontinuous and continuous), there are no issues. What is the reason for such behavior? Is there a way to fix this? Thank you, Aidyn

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Orthogonalization of polynomial coefficients / mass-matrix access from solver level
by Vidhi Zala 18 Jun '19

18 Jun '19

Hi all, If anyone has come across the application in Nektar++ that requires polynomial coefficients to be orthogonalized or know how to access mass matrix using m_fields[] within solver, please point me to the example code. Thank you for help, Vidhi -- ,-~~-.___. ._. / | ' \ | |--------. 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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womersley number
by Shanshan Luo 18 Jun '19

18 Jun '19

Dear all, I'm confused about description of womersley number on Page 150 of user-guide-4.4.1. Can anyone give me some suggestions? On Page 150, for the formulas below: [image: Screen Shot 2019-06-15 at 5.20.02 PM.png] [image: Screen Shot 2019-06-15 at 5.20.11 PM.png] How can I calculate *'alpha'*? Or it is a typo and should be *'alpha_n'*? Also for the formula : [image: Screen Shot 2019-06-15 at 5.23.19 PM.png], what does *R* and *T *represent? Does R mean RADIUS (the non-dimensional radius of the boundary in Gmsh) or the real radius (with dimension) of the object? Does T mean Period (the non-dimensional cycle time period)? Thank you very much! Best, Shan

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Running IncNavierStokesSolver in parallel with I.C. from file
by Akhavan Safaei, Ali 07 Jun '19

07 Jun '19

Hello everyone, I got an issue when I want to run IncNavierStokesSolver while I am giving the initial conditions from a filed data file as: <FUNCTION NAME="InitialConditions"> <F VAR="u,v,w,p" FILE="IC.fld"/> </FUNCTION> The "IC.fld" was generated from the following interpolation using parallel FieldConvert: mpirun -np 256 FieldConvert -m interppointdatatofld Grid.xml IC.pts IC.fld where "IC.pts" comes from u,v,w,p from a fully turbulent 3D data. When I'm running the IncNavierStokesSolver with the following command: mpirun -np 256 IncNavierStokesSolver Grid.xml Conds.xml I'm getting the following error: Fatal : Level 0 assertion violation A parallel solver must be used when run in parallel. ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code. Per user-direction, the job has been aborted. ------------------------------------------------------- -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Exit code: 1 -------------------------------------------------------------------------- Everything works correctly if I don't run in parallel. Has anybody seen such issue? I would extremely appreciate it if you can help me with that. Kind Regards, Ali Akhavan-Safaei --------------------------------------------------- --------------------------------------------------- Ali Akhavan-Safaei, PhD student, Graduate Research Assistant Michigan State University Department of Mechanical Engineering 428 S. Shaw Lane Engineering Bldg., Rm. #4110 East Lansing, MI 48824 Email: akhavans(a)msu.edu akhavans(a)egr.msu.edu --------------------------------------------------- ---------------------------------------------------

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Re: [Nektar-users] FieldConvert: extract module
by Shanshan Luo 07 Jun '19

07 Jun '19

Dear professor Sherwin, Many thanks to your reply and explanation. My problem is solved. Best, Shan On Thu, Jun 6, 2019 at 2:45 AM Sherwin, Spencer J <s.sherwin(a)imperial.ac.uk> wrote: > Hi Shan, > > You can simply specify the name of the folder or file. Internally we check > to see the nature of the filename (a file or directory) and load it > accordingly. So just treat it as if it were a file. > > In Nektar 5.0 we are moving to a HDF5 format although we will also support > this type of format too. > > Cheers, > Spencer > > Sent from my iPhone > > On 6 Jun 2019, at 07:04, Shanshan Luo <luoss(a)sas.upenn.edu> wrote: > > Dear Professor Sherwin, > > Thank you for you reply! > Apologize for not giving clear explanation to my 'chk file'. Actually, " > cylinder1_Spherigon_5.chk" is a folder. It contains several fld files as > shown below: > <Screen Shot 2019-06-06 at 1.59.59 AM.png> > I get it due to using mpirun command to do simulation. > > May I know how can I deal with such .chk file? > > > Thank you a lot again! > > > Best, > > Shan > > On Thu, Jun 6, 2019 at 1:49 AM Sherwin, Spencer J < > s.sherwin(a)imperial.ac.uk> wrote: > >> Hi Shan, >> >> I presume you were running a command like: >> >> FieldConvert -m extract:bnd=1 cylinder1_Spherigon.xml >> cylinder1_Spherigon_5.chk cylinder1_Spherigon_5-boundary.chk >> >> The ‘bnd’ here is just shorthand for the boundary region defined in the >> condition setup of your run. >> >> I wonder if you have included the <CONDITION> section in your >> cylinder1_Spherigon.xml file? Or is there another file with the information >> about boundary conditions that you would normally use when running the >> simulation. I think this error may reflect that it is trying to find the >> boundary 1 (i.e. bnd=1) but it is not defined since this information is not >> included in the xml file you have provided? >> >> It should be fine to use the ending chk it is treated just the same as fld >> >> Cheers, >> Spencer. >> >> On 5 Jun 2019, at 21:14, Shanshan Luo <luoss(a)sas.upenn.edu> wrote: >> >> Dear all, >> >> When I run the command: >> FieldConvert -m extract:fldtoboundary=1 cylinder1_Spherigon.xml >> cylinder1_Spherigon_5.chk cylinder1_Spherigon_5-boundary.chk >> >> It gives out errors: >> Fatal : Level 0 assertion violation >> Variable index out of range. >> libc++abi.dylib: terminating with uncaught exception of type >> ErrorUtil::NekError: Level 0 assertion violation >> Variable index out of range. >> Abort trap: 6 >> >> I want to know can this command run with .chk file? Since we use the >> parallel computing, our cylinder1_Spherigon_5.chk file contains several >> .fld files and one info.xml. >> >> Also I want to know for the command in Page 84 of user-guide-4.4.1, >> what does "bnd" really mean? >> >> Could you help me figure this out? Thank you very much! >> >> Best, >> Shan >> _______________________________________________ >> 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/ >> >>

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FieldConvert: extract module
by Shanshan Luo 07 Jun '19

07 Jun '19

Dear all, When I run the command: FieldConvert -m extract:fldtoboundary=1 cylinder1_Spherigon.xml cylinder1_Spherigon_5.chk cylinder1_Spherigon_5-boundary.chk It gives out errors: Fatal : Level 0 assertion violation Variable index out of range. libc++abi.dylib: terminating with uncaught exception of type ErrorUtil::NekError: Level 0 assertion violation Variable index out of range. Abort trap: 6 I want to know can this command run with .chk file? Since we use the parallel computing, our cylinder1_Spherigon_5.chk file contains several .fld files and one info.xml. Also I want to know for the command in Page 84 of user-guide-4.4.1, what does "bnd" really mean? Could you help me figure this out? Thank you very much! Best, Shan

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ADRsolver
by Stanisław Gepner 06 Jun '19

06 Jun '19

Hi all, Can somebody tell me if the ADRsolver can handle: 1. AdvectionVelocity from a set of files i.e. TIMEDEPENDENT: <FUNCTION NAME="AdvectionVelocity">  <F VAR="Vx,Vy,Vz" TIMEDEPENDENT="1" FILE="geom_%03i.chk:u,v,w" />  </FUNCTION> It seems as if it just uses the first file (or I am doing sth. wrong). I looked into the UnsteadyAdvection.cpp and AdvectionVelocity seems to be evaluated only at initialization. Is it the case? 2. Have Forcing f from a file: <FUNCTION NAME="Forcing"> <F VAR="Q" FILE="geom_240.chk:Q" /> </FUNCTION> For the above I am getting: Fatal : Level 0 assertion violation Function is defined by a file. Stan

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FieldConvert: extract module for parallel computing results
by Shanshan Luo 05 Jun '19

05 Jun '19

Dear all, I try to extract boundary region by running: FieldConvert -m extract:fldtoboundary=1 cylinder1_Spherigon.xml cylinder1_Spherigon_5.chk cylinder1_Spherigon_5-boundary.chk Here my cylinder1_Spherigob_5.chk is a folder which contains: [image: Screen Shot 2019-06-05 at 6.06.53 PM.png] This is due to we use mpirun command to do simulation. However, we get the errors when running the above command: Fatal : Level 0 assertion violation Variable index out of range. libc++abi.dylib: terminating with uncaught exception of type ErrorUtil::NekError: Level 0 assertion violation Variable index out of range. Abort trap: 6 May I know how can I deal with such .chk file? Thank you very much! Best, Shan

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Re: [Nektar-users] Possibility of adding velocity dependent terms to the existing Incompressible Navier Stokes solver
by Swagat Kumar Nayak 31 May '19

31 May '19

Hi, Thanks for the reply. I think I should be able to do that. Thanks again! Swagat On Fri, May 31, 2019, 7:03 PM Stanisław Gepner <sgepner(a)meil.pw.edu.pl> wrote: > Hi Swagat, > > The MovingReferenceFrame has been implemented only for constant > velocity of the Frame. That is it can not be a function of time and > space. So I am afraid it will not work the way you are trying to do it > here, only by putting appropriate values in the xml file. > > What I meant is, that if you know what terms you need to add to the NS > equation, you could manipulate the source of Nektar - essentially write > a new Forcing function - very mych like the MovingReferenceFrame is > written. There the NS equation is supplemented by sth. like > > c_x * \partial u / \partial x > > with c_x the speed of the moving frame. > > Cheers, > Stan > > On pią, 2019-05-31 at 18:20 +0900, Swagat Kumar Nayak wrote: > > Hi Stanisław, > > > > Thanks for your reply. I checked the files. I think that if I add the > > frame velocity and the appropriate Initial and Boundary conditions, > > then I hope that it should work for me. Though, I am unsure about its > > implementation. Does the way I am implementing it, seem correct? > > > > <NEKTAR> > >  > > <EXPANSIONS> > > ............................. > > </EXPANSIONS> > > > >  > > <FILTERS> > > ............................. > > </FILTERS> > > > >  > > <CONDITIONS> > > <SOLVERINFO> > > .............................. > > </SOLVERINFO> > > > > <PARAMETERS> > > ............................. > > </PARAMETERS> > > > >  > > > > <VARIABLES> > > <V ID="0"> u </V> > > <V ID="1"> v </V> > > <V ID="2"> w </V> > > <V ID="3"> p </V> > > </VARIABLES> > > > >  > > <BOUNDARYREGIONS> > > ........................................ > > </BOUNDARYREGIONS> > > > > <BOUNDARYCONDITIONS> > > ................................................. > > </BOUNDARYCONDITIONS> > > > >  > > > > <FUNCTION NAME="InitialConditions"> > > <E VAR="u" VALUE="F(y)" /> > > <E VAR="v" VALUE="G(x)" /> > > <E VAR="w" VALUE="0" /> > > <E VAR="p" VALUE="0" /> > > </FUNCTION> > > > > <FORCE TYPE="MovingReferenceFrame"> > > <FRAMEVELOCITY> > > <FUNCTION NAME="MovingReferenceFrame"> > > <E VAR="u" VALUE="f(y,z,t)" /> > > <E VAR="v" VALUE="g(y,z,t)" /> > > <E VAR="w" VALUE="0" /> > > </FUNCTION> > > <FRAMEVELOCITY/> > > </FORCE> > > > > </CONDITIONS> > > </NEKTAR> > > > > Thank you ! > > Swagat Kumar Nayak > > > > On Wed, May 29, 2019 at 7:14 PM Stanisław Gepner < > > sgepner(a)meil.pw.edu.pl> wrote: > > > Hi Swagat, > > > > > > Not sure anyone answered this. > > > > > > 1) You could try to add a Forcing term. Much like ForcingBody in > > > library/Solverutils/Forcing. I think something similar to what you > > > describe has been done for the moving reference frame > > > (ForcingMovingReferenceFrame) i.e. additional terms that are > > > gradient > > > of velocity. > > > > > > 2) At the end of the .geo file there is a protion where Physical > > > objects are declared. Sth. like: > > > > > > Physical Line(1) = {3,1,2,4}; > > > Physical Surface(2) = {6}; > > > > > > My experience with NekMesh is that composite 2 is the 2D domain and > > > composite 1 the boundary. > > > > > > Cheers, > > > Stan > > > > > > On czw, 2019-05-23 at 14:25 +0900, Swagat Kumar Nayak wrote: > > > > Hi everyone, > > > > > > > > I am trying to simulate the flow of a precessing cylinder in the > > > > cylinder frame of reference. I have got some additional terms in > > > the > > > > incompressible Navier-stokes equation which are velocity > > > dependent. > > > > (1) How do I add these additional terms to the incompressible > > > Navier- > > > > stokes equation? > > > > > > > > (2) When I create a mesh in Gmsh and try to convert it into the > > > .xml > > > > file format, how do I identify the composites corresponding to > > > the > > > > global boundaries? > > > > > > > > I am new to this framework. So, any help will be largely > > > appreciated. > > > > > > > > > > > > Thank you, > > > > > > > > _______________________________________________ > > > > Nektar-users mailing list > > > > Nektar-users(a)imperial.ac.uk > > > > https://mailman.ic.ac.uk/mailman/listinfo/nektar-users > > > > > > > > >

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Implementation of Force Type "MovingReferenceFrame" in Nektar++
by Swagat Kumar Nayak 31 May '19

31 May '19

Hi all, I intend to solve the Incompressible Navier Stokes equations in a rotating reference frame. Hence, I am adding the frame velocity of the rotating frame as a Force Type = "MovingReferenceFrame". Will it add the appropriate Coriolis term? Also, does the implementation seem correct? <NEKTAR>  <EXPANSIONS> ............................. </EXPANSIONS>  <FILTERS> ............................. </FILTERS>  <CONDITIONS> <SOLVERINFO> .............................. </SOLVERINFO> <PARAMETERS> ............................. </PARAMETERS>  <VARIABLES> <V ID="0"> u </V> <V ID="1"> v </V> <V ID="2"> w </V> <V ID="3"> p </V> </VARIABLES>  <BOUNDARYREGIONS> ........................................ </BOUNDARYREGIONS> <BOUNDARYCONDITIONS> ................................................. </BOUNDARYCONDITIONS>  <FUNCTION NAME="InitialConditions"> <E VAR="u" VALUE="F(y)" /> <E VAR="v" VALUE="G(x)" /> <E VAR="w" VALUE="0" /> <E VAR="p" VALUE="0" /> </FUNCTION> <FORCE TYPE="MovingReferenceFrame"> <FRAMEVELOCITY> <FUNCTION NAME="MovingReferenceFrame"> <E VAR="u" VALUE="f(y,z,t)" /> <E VAR="v" VALUE="g(y,z,t)" /> <E VAR="w" VALUE="0" /> </FUNCTION> <FRAMEVELOCITY/> </FORCE> </CONDITIONS> </NEKTAR> Thank you ! -- *Swagat Kumar Nayak * *Department of Mechanical Engineering* *IIT Kharagpur*

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