March 2019 - Nektar-users - imperial.ac.uk

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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compressible flow solver scalability with fortran subroutines
by Arash Nouri 20 Apr '19

20 Apr '19

Hi all, I've added an equation of state and a chemical reaction to the compressible flow solver via couple of FORTRAN subroutines. In my 2D simulations, everything is cool and I've almost linear scalability up to 2K processors. However, my 3D simulations are surprisingly slow. Do you have any idea about probable reasons? What I basically do for the chemical reaction is: I call a FORTRAN subroutine in DoOdeRhs to get the required forcing terms for energy and species equations. Best, Arash --------------------------------- Arash G. Nouri Research Scientist Computational Modeling & Simulation (http://cmsp.pitt.edu/) 1127 Benedum Hall University of Pittsburgh Pittsburgh, PA 15261, USA E-mail: arn36(a)pitt.edu

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CG iterations made = 5001 using tolerance of 1e-09 (error = nan, rhs_mag = inf) error
by Moto Light 24 Mar '19

24 Mar '19

Hi All, i am runing simple case at Re1000, i tried many meshs all of them give me the same error ////////////////////// Steps: 91200 Time: 424.694 CPU Time: 4.48716s Steps: 91210 Time: 424.695 CPU Time: 4.62339s *CG iterations made = 5001 using tolerance of 1e-09 (error = nan, rhs_mag = inf)* *job ended at* ///////////////////////////// any suggestions? my case file /////////////////////////////////////////// <?xml version="1.0" encoding="UTF-8" ?> <NEKTAR> <EXPANSIONS> <E COMPOSITE="C[1]" NUMMODES="6" FIELDS="u,v,w,p" TYPE="MODIFIED" />  <E COMPOSITE="C[2]" NUMMODES="6" FIELDS="u,v,w,p" TYPE="MODIFIED" />  <E COMPOSITE="C[3]" NUMMODES="6" FIELDS="u,v,w,p" TYPE="MODIFIED" />  <E COMPOSITE="C[4]" NUMMODES="6" FIELDS="u,v,w,p" TYPE="MODIFIED" />  <E COMPOSITE="C[5]" NUMMODES="6" FIELDS="u,v,w,p" TYPE="MODIFIED" />  <E COMPOSITE="C[6]" NUMMODES="6" FIELDS="u,v,w,p" TYPE="MODIFIED" />  <E COMPOSITE="C[7]" NUMMODES="6" FIELDS="u,v,w,p" TYPE="MODIFIED" />  <E COMPOSITE="C[8]" NUMMODES="6" FIELDS="u,v,w,p" TYPE="MODIFIED" />  </EXPANSIONS> <CONDITIONS> <SOLVERINFO>  </SOLVERINFO> <PARAMETERS> TimeStep = 0.0001 NumSteps = 2500000  IO_CheckSteps = 5000  IO_InfoSteps = 10 Re = 200 Kinvis = 1./Re IO_CFLSteps = 50 LZ = 9  HomModesZ = 32  </PARAMETERS> <VARIABLES> <V ID="0"> u </V> <V ID="1"> v </V> <V ID="2"> w </V> <V ID="3"> p </V> </VARIABLES> <BOUNDARYREGIONS> C[9]  C[10]  C[11]  C[12]  C[13]  C[14]  C[15]  </BOUNDARYREGIONS> <BOUNDARYCONDITIONS> <REGION REF="0">  <D VAR="u" VALUE="5" /> <D VAR="v" VALUE="0" /> <D VAR="w" VALUE="0" /> <N VAR="p" USERDEFINEDTYPE="H" VALUE="0"/> </REGION> <REGION REF="1">  <D VAR="u" VALUE="1" /> <D VAR="v" VALUE="0" /> <D VAR="w" VALUE="0" /> <N VAR="p" USERDEFINEDTYPE="H" VALUE="0"/> </REGION> <REGION REF="2">  <D VAR="u" VALUE="0" /> <D VAR="v" VALUE="0" /> <D VAR="w" VALUE="0" /> <N VAR="p" USERDEFINEDTYPE="H" VALUE="0" /> </REGION> <REGION REF="3">  <N VAR="u" USERDEFINEDTYPE="H" VALUE="0" /> <D VAR="v" VALUE="0" /> <N VAR="w" USERDEFINEDTYPE="H" VALUE="0" /> <N VAR="p" USERDEFINEDTYPE="H" VALUE="0" /> </REGION> <REGION REF="4">  <N VAR="u" USERDEFINEDTYPE="H" VALUE="0" /> <D VAR="v" VALUE="0" /> <N VAR="w" USERDEFINEDTYPE="H" VALUE="0" /> <N VAR="p" USERDEFINEDTYPE="H" VALUE="0" /> </REGION> <REGION REF="5">  <N VAR="u" USERDEFINEDTYPE="HOutflow" VALUE="0" /> <N VAR="v" USERDEFINEDTYPE="HOutflow" VALUE="0" /> <N VAR="w" USERDEFINEDTYPE="HOutflow" VALUE="0" /> <D VAR="p" USERDEFINEDTYPE="HOutflow" VALUE="0" /> </REGION> <REGION REF="6">  <D VAR="u" VALUE="0" /> <D VAR="v" VALUE="0" /> <D VAR="w" VALUE="0" /> <N VAR="p" USERDEFINEDTYPE="H" VALUE="0" /> </REGION> </BOUNDARYCONDITIONS>  <FUNCTION NAME="InitialConditions"> <E VAR="w" VALUE="awgn(1e-3)*cos(2*PI*z/LZ)" />   <F VAR="u,v,p" FILE="SquareN2D_200.chk" />  </FUNCTION> <FUNCTION NAME="ExactSolution"> <E VAR="u" VALUE="0" /> <E VAR="v" VALUE="0" /> <E VAR="w" VALUE="0" /> <E VAR="p" VALUE="0" /> </FUNCTION> </CONDITIONS> <FILTERS> <FILTER TYPE="AeroForces"> <PARAM NAME="OutputFile">stats/stats1/CylinderForces3D</PARAM> <PARAM NAME="OutputFrequency">10</PARAM> <PARAM NAME="Boundary"> B[6] </PARAM> </FILTER> </FILTERS> </NEKTAR> ///////////////////////////////// please help me in this Regrads, cheers, Reda PhD student Aerospace department UPC Barcelona

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Problem with SolveSteadyNavierStokes() in Nektar++-4.4.0
by Moreno Pintore S252841 22 Mar '19

22 Mar '19

In version 4.4.0 I wold like to use the SolveSteadyNavierStokes() function to solve my system with the Newton method but it always returns a similar output: L2Norm[0] = -nan L2Norm[1] = -nan Is the method working in that version (because I didn't found it in the documentation)? Do I have to initialize in some particular way the m_fields variable? At the moment I initialized each field with zeros but I don't understand if I have to do something else. Thank you, Moreno Pintore

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Gmsh mesh seems fine, but Nekmesh points out error
by Icaro Amorim de Carvalho 21 Mar '19

21 Mar '19

Hi all, I'm using Nektar+ 4.4.1 and have run Gmsh 4.1.3, 4.1.4 and 4.1.5. When I generate the mesh it seems to be fine on all Gmsh versions. No error output on my .msh file whatsoever. However, when I use Nekmesh to generate the .xml file the following error emerges (both for compressed and uncompressed conversion): [image: image.png] Could any one provide some input on how do I solve this? Sds, *Icaro Amorim de Carvalho*. *Master's candidate* * in Mechanical Engineering* *University of São Paulo - Escola Politécnicaamorim.icaro(a)usp.br <amorim.icaro(a)usp.br>*

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collecting Reynolds average stresses
by Vishal Saini 21 Mar '19

21 Mar '19

Hi all, I'm running an SVV LES simulation using the IncNavierStokesSolver. Ran the initialisation bit and finally started collecting the statistics using the filter below: * <FILTER TYPE="ReynoldsStresses"> <PARAM NAME="OutputFile">AverageField_0pt1sOnwards</PARAM> <PARAM NAME="OutputFrequency">1000</PARAM> <PARAM NAME="SampleFrequency">1</PARAM> </FILTER>* Checked the <uu> component on a sliced plane and it looked fine (top figure in the attachment). However, when I resume the simulation using the last written Average Field and the chk file as a starting point, the <uu> (and the other components) looks a bit corrupted (bottom figure in the attachment). * <FILTER TYPE="ReynoldsStresses"> <PARAM NAME="OutputFile">AverageField_0pt5sOnwards</PARAM> <PARAM NAME="RestartFile">AverageField_0pt1sOnwards_stress.fld</PARAM> <PARAM NAME="OutputFrequency">1000</PARAM> <PARAM NAME="SampleFrequency">1</PARAM> </FILTER>* May be I'm missing something! Has anyone encountered this before? If yes, is there a workaround? PS. Average velocities look similar in the two cases. BR, Vishal

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Please Help, creating Buffer zone, or use another outlet BC
by Moto Light 20 Mar '19

20 Mar '19

Hi All, I am simulating a 3D case and my case was working fine in 2D, after run it in 3D it keeps crashing. I have a serious problem in the outlet BC and I tried to use higher order BC and still crashing My case outlet BC is -------------------------------------------- <REGION REF="5">  <N VAR="u" USERDEFINEDTYPE="HOutflow" VALUE="0" /> <N VAR="v" USERDEFINEDTYPE="HOutflow" VALUE="0" /> <N VAR="w" USERDEFINEDTYPE="HOutflow" VALUE="0" /> <D VAR="p" USERDEFINEDTYPE="HOutflow" VALUE="0" /> </REGION> ----------------------------------------------- any suggestions? Also if i can creat a buffer zone how i can do it with different viscosity, or can i specify "SpectralVanishingViscosity" to a specific zone not for all the domain. Regards, Cheers, Reda PhD student Aerospace Dep UPC Spain

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Hi all error ending my simulation
by Moto Light 20 Mar '19

20 Mar '19

Hi All, i am runing simple case at Re1000, i tried many meshs all of them give me the same error ////////////////////// Steps: 91200 Time: 424.694 CPU Time: 4.48716s Steps: 91210 Time: 424.695 CPU Time: 4.62339s CG iterations made = 5001 using tolerance of 1e-09 (error = nan, rhs_mag = inf) job ended at ///////////////////////////// any suggestions? my case file /////////////////////////////////////////// <?xml version="1.0" encoding="UTF-8" ?> <NEKTAR> <EXPANSIONS> <E COMPOSITE="C[1]" NUMMODES="6" FIELDS="u,v,w,p" TYPE="MODIFIED" />  <E COMPOSITE="C[2]" NUMMODES="6" FIELDS="u,v,w,p" TYPE="MODIFIED" />  <E COMPOSITE="C[3]" NUMMODES="6" FIELDS="u,v,w,p" TYPE="MODIFIED" />  <E COMPOSITE="C[4]" NUMMODES="6" FIELDS="u,v,w,p" TYPE="MODIFIED" />  <E COMPOSITE="C[5]" NUMMODES="6" FIELDS="u,v,w,p" TYPE="MODIFIED" />  <E COMPOSITE="C[6]" NUMMODES="6" FIELDS="u,v,w,p" TYPE="MODIFIED" />  <E COMPOSITE="C[7]" NUMMODES="6" FIELDS="u,v,w,p" TYPE="MODIFIED" />  <E COMPOSITE="C[8]" NUMMODES="6" FIELDS="u,v,w,p" TYPE="MODIFIED" />  </EXPANSIONS> <CONDITIONS> <SOLVERINFO>  </SOLVERINFO> <PARAMETERS> TimeStep = 0.0001 NumSteps = 2500000  IO_CheckSteps = 5000  IO_InfoSteps = 10 Re = 200 Kinvis = 1./Re IO_CFLSteps = 50 LZ = 9  HomModesZ = 32  </PARAMETERS> <VARIABLES> <V ID="0"> u </V> <V ID="1"> v </V> <V ID="2"> w </V> <V ID="3"> p </V> </VARIABLES> <BOUNDARYREGIONS> C[9]  C[10]  C[11]  C[12]  C[13]  C[14]  C[15]  </BOUNDARYREGIONS> <BOUNDARYCONDITIONS> <REGION REF="0">  <D VAR="u" VALUE="5" /> <D VAR="v" VALUE="0" /> <D VAR="w" VALUE="0" /> <N VAR="p" USERDEFINEDTYPE="H" VALUE="0"/> </REGION> <REGION REF="1">  <D VAR="u" VALUE="1" /> <D VAR="v" VALUE="0" /> <D VAR="w" VALUE="0" /> <N VAR="p" USERDEFINEDTYPE="H" VALUE="0"/> </REGION> <REGION REF="2">  <D VAR="u" VALUE="0" /> <D VAR="v" VALUE="0" /> <D VAR="w" VALUE="0" /> <N VAR="p" USERDEFINEDTYPE="H" VALUE="0" /> </REGION> <REGION REF="3">  <N VAR="u" USERDEFINEDTYPE="H" VALUE="0" /> <D VAR="v" VALUE="0" /> <N VAR="w" USERDEFINEDTYPE="H" VALUE="0" /> <N VAR="p" USERDEFINEDTYPE="H" VALUE="0" /> </REGION> <REGION REF="4">  <N VAR="u" USERDEFINEDTYPE="H" VALUE="0" /> <D VAR="v" VALUE="0" /> <N VAR="w" USERDEFINEDTYPE="H" VALUE="0" /> <N VAR="p" USERDEFINEDTYPE="H" VALUE="0" /> </REGION> <REGION REF="5">  <N VAR="u" USERDEFINEDTYPE="HOutflow" VALUE="0" /> <N VAR="v" USERDEFINEDTYPE="HOutflow" VALUE="0" /> <N VAR="w" USERDEFINEDTYPE="HOutflow" VALUE="0" /> <D VAR="p" USERDEFINEDTYPE="HOutflow" VALUE="0" /> </REGION> <REGION REF="6">  <D VAR="u" VALUE="0" /> <D VAR="v" VALUE="0" /> <D VAR="w" VALUE="0" /> <N VAR="p" USERDEFINEDTYPE="H" VALUE="0" /> </REGION> </BOUNDARYCONDITIONS>  <FUNCTION NAME="InitialConditions"> <E VAR="w" VALUE="awgn(1e-3)*cos(2*PI*z/LZ)" />   <F VAR="u,v,p" FILE="SquareN2D_200.chk" />  </FUNCTION> <FUNCTION NAME="ExactSolution"> <E VAR="u" VALUE="0" /> <E VAR="v" VALUE="0" /> <E VAR="w" VALUE="0" /> <E VAR="p" VALUE="0" /> </FUNCTION> </CONDITIONS> <FILTERS> <FILTER TYPE="AeroForces"> <PARAM NAME="OutputFile">stats/stats1/CylinderForces3D</PARAM> <PARAM NAME="OutputFrequency">10</PARAM> <PARAM NAME="Boundary"> B[6] </PARAM> </FILTER> </FILTERS> </NEKTAR> ///////////////////////////////// please help me in this Regrads, cheers, Reda PhD student Aerospace department UPC Barcelona

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FieldConvert interpfield odd behaviour
by Raposo, Henrique T 18 Mar '19

18 Mar '19

Hello everyone, I'm using the FieldConvert interpfield function to interpolate a simple inviscid flow around a Joukowski airfoil onto a new mesh. While for the most part the result seems to be smooth and correct when visualizing the field in paraview, there are a few odd isolated cells wherein the interpolated values in the new mesh are completely off. The files to reproduce this behaviour are too big to share here, but I'm sending a screenshot to illustrate this. I'm using Nektar++ 4.4.1 and performing the computation in parallel. Any help understanding this would be much appreciated. Cheers, Henrique

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Adaptive Selective frequency damping method for flow past cylinder at Re 100.
by wasim sarwar 17 Mar '19

17 Mar '19

Dear all, I have been trying to use Selective frequency damping (SFD) method adopted in the SteadyState Driver, in order to get an unstable steady state solution whose stability is to be determined. I see in the nektar++ user guide there are two approaches: classical one, and the adaptedSFD. I am trying to validate the case of flow past circular cylinder at Re=100 studied by Jordi link herein https://spiral.imperial.ac.uk/bitstream/10044/1/31875/.../Jordi-B-2016-PhD-… <https://spiral.imperial.ac.uk/bitstream/10044/1/31875/3/Jordi-B-2016-PhD-Th…> . With the values of growth rate and frequency mentioned in this thesis, i am able to achieve convergence upto O(-8) for the classical approach. The problem arises when I use AdaptedSFD method. Initially, AdaptedSFD runs smoothly untill tolerance O(-2), then it switches to stability analysis to estimate growth rate and frequency which is used to predict next value of control coefficient and filter width. The problem lies in the estimation of growth rate and frequency which give nonphysical large values of order 10. I have attached the Session.xml, Session_LinNS.xml, and output results generated. Any help is highly appreciated. Cheers Wasim

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