October 2016 - Nektar-users

Implementation of damping zones
by Selbach, Fabian 25 Oct '16

25 Oct '16

Dear Community, I would like to know more about how to implement damping-zones in detail. Of course I already found the example with the following structure, but no other information about the mathematical background of this "Absorption-Forcing" and the definitions of RefFields and SpongeCoeffizient :  <FUNCTION NAME="RefFields"> <E VAR="u" VALUE="-y*y+1" /> <E VAR="v" VALUE="0" /> <E VAR="p" VALUE="0" /> </FUNCTION> <FUNCTION NAME="SpongeCoefficient"> <E VAR="u" VALUE="-100*(x>2.5)" /> <E VAR="v" VALUE="-100*(x>2.5)" /> </FUNCTION> </CONDITIONS> <FORCING> <FORCE TYPE="Absorption"> <COEFF> SpongeCoefficient </COEFF> <REFFLOW> RefFields </REFFLOW> </FORCE> </FORCING> With the SpongeCoefficient function I define the space where my sponge zone starts, am I right? So in this example it starts from x>2.5, but what about the -100? Is it some kind of function like u _damp = -100*u*(-y*y+1)? I'm not sure about that and there are no information in the user-guide. Can somebody explain that in more detail? And do I have to care any other modifications? Thanks for any answer! Best regards Fabian

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about interppoints
by Asim Onder 21 Oct '16

21 Oct '16

Dear Nektar users/developers, I’m doing some simulations in 3D1H, and trying to extract data along a line in homogenous direction using interppoints module. However, the output contains constant data, shows no variation along the points. I was wondering if interppoints contains a bug or I’m just doing something wrong. Here is the command I used, and I also attached the config file and the output. FieldConvert -v -m interppoints:fromxml=config.xml:fromfld=fields/field_48.chk:line=1080,0.0884,0.009,0,0.0884,0.009,0.406 pointData/kMax_48.dat Thank you very much in advance for any feedback. Best, Asim P.S.: i had some troubles while sending this e-mail, sorry if you received this message multiple times. ________________________________ Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you.

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(no subject)
by Mengaldo, Gianmarco 18 Oct '16

18 Oct '16

Hi Fabian, you can actually run in verbose mode ./executable -v file.xml to see additional parameters, such as the operator evaluation. Regarding the most appropriate hp space, this depends on the case. For the Nan, I would suggest that you try to increase the number of quadrature points while keeping the number of modes fixed. A second possibility is that you start the simulation non-impulsively but using a ramp in time for the farfield boundary conditions. Regards, Gianmarco Gianmarco Mengaldo Department of Aeronautics and Mathematics Imperial College London South Kensington Campus SW7 2AZ, London, UK ***Currently at Caltech From: "Selbach, Fabian" <fabian.selbach(a)student.uni-siegen.de<mailto:fabian.selbach@student.uni-siegen.de>> Subject: [Nektar-users] Default operator evaluation in Nektar++ and error "NaN found during time integration" Date: 10 October 2016 at 14:09:28 BST To: "nektar-users(a)imperial.ac.uk<mailto:nektar-users@imperial.ac.uk>" <nektar-users(a)imperial.ac.uk<mailto:nektar-users@imperial.ac.uk>> Dear Nektar++ -Community, please can you tell me the default operator evaluation in Nektar++? In the papers "From h to p efficiently" there are mentioned three kind of types: 1. global matrix approach 2. local matrix approach 3. sum-factorization I want to choose the best hp/ configuration for my 3D simulation and this -of course- depends on the operator evaluation strategy. I think actually Nektar++ uses the global matrix approach by default, but I'm not sure by 100%. My second question depends on the error message: "Fatal : Level 0 assertion violation NaN found during time integration." While using this configuration: ======================================================================= EquationType: EulerCFE Session Name: 3Dmeshcube_h10 Spatial Dim.: 3 Max SEM Exp. Order: 3 Num. Processes: 24 Expansion Dim.: 3 Riemann Solver: HLLC Advection Type: Projection Type: Discontinuous Galerkin Diffusion Type: Advection: explicit AdvectionType: WeakDG Diffusion: explicit Time Step: 0.01 No. of Steps: 10000 Checkpoints (steps): 1000 Integration Type: RungeKutta2_ImprovedEuler Problem Type: General ======================================================================= Initial Conditions: - Field rho: rhoInf + (0.01 * exp(-0.077*(x^2 + y^2 + z^2))) - Field rhou: rhoInf * uInf - Field rhov: rhoInf * vInf - Field rhow: rhoInf * wInf - Field E: (pInf / (Gamma - 1)) + ((rhoInf/2) * uInf^2) + ((0.01/(Gamma-1))*exp(-0.077*(x^2 + y^2 + z^2))) +( (0.01/2) * uInf^2 * exp(-0.077*(x^2 + y^2 + z^2))) I already changed my time-step and the refinement of my mesh and i think this error message is because of oscillation of my solution. So maybe my mesh is not fine enough or i must increase p. But i want to use a fix h to p constellation to test the efficiency. Can anybody help me with this problem? I already tried to use the spectral hp dealiasing, the smooth advection and artificial viscosity, but it doesn't worked or helped... Thanks for any answer. Best regards Fabian _______________________________________________ Nektar-users mailing list Nektar-users(a)imperial.ac.uk<mailto:Nektar-users@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/nektar-users

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Output of L2 and LInf norms during simulation
by Selbach, Fabian 18 Oct '16

18 Oct '16

Dear Nektar++ community, I would like to know how it's possible to get the L2 and LInf norms during a simulation at every InfoStep and not only at the end of a simulation? Is there an easy way to do so? The postprocessing tool of fieldconvert just can do it at every CheckStep and to do so I will have to do it very often and I always need a chk.-file. Furthermore (maybe it's a bug) the postprocessing module "printfldnorms" of fieldconvert always compares to an exact solution of 0 and never to the given exact solution (but the ouput file of the solver itself compares the exact solution - so there is only a bug in the postprocessing tool). I hope I will get an answer. Thank you. Best regards Fabian Selbach

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Unphysical pressure oscillations
by F Mellibovsky 18 Oct '16

18 Oct '16

Dear all, I have been trying to set up a time-dependent 2D external flow incompressible Navier-Stokes computation in the transitional regime (separated flow around airfoil at Re~5000, aoa=12) but I get unphysical pressure oscillations across the domain. The main features of the flow, vortex shedding frequency, aerodynamic forces mean value and oscillation amplitude are captured with reasonable resolution. There appear, however, high frequency pressure oscillations whose amplitude is reduced by an increase in resolution without ever completely disappearing. The velocity field seems to be little affected by this pressure oscillations, but they are however quite annoying. I have tried, but doesn't seem to have any effect whatsoever: - many different meshes - usual outlet boundary conditions (Neumann for velocity, Dirichlet for pressure) and HOutflow BC. - nodal and modal expansions. (btw, what is the difference between GLL_Lagrange and GLL_Lagrange_SEM?) - convective and skew-symmetric forms for the advection term - 1st 2nd and 3rd order time integration with the IMEX time-stepper - Reducing the timestep Dealiasing with SpectralHPDealiasing has some effect, but not much. What seems to work quite well in smoothing the pressure oscillations is using SmoothAdvection (I am not sure of what this does), except that the computation eventually destabilises and produces NaNs. I also wanted to try the inf-sup condition and use different expansion orders for pressure and velocity, but this does not seem to be possible other than with the direct solver, which cannot be used for fully nonlinear transient computations. Another option I considered was using the unconditionally stable rotational velocity-correction scheme of Dong & Shen (JCP 2010) but I think it is not implemented in the IncNavierStokesSolver. Please find attached the files to run one of the many tests I have performed. Any help will be welcome. Many thanks in advance. Cheers, Fer

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complex mode in linear stability analysis
by Hongfu Zhang 18 Oct '16

18 Oct '16

Dear, All I would like to know if the leading mode are complex mode in linear stability analysis, what part doses the code output to Paraview ? real part or imaginary part or normal part? Thanks very much for any help! Hongfu

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Which file in the director depicting how to apply boundary conditions for the diffusion equations.
by 丁老师 16 Oct '16

16 Oct '16

Dear Nektar group: I Want to know the method of applying first, and second BC for the diffusion equations. Which file in the source directory deicting about this. Regards Your Sincerely Ding

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Default operator evaluation in Nektar++ and error "NaN found during time integration"
by Selbach, Fabian 10 Oct '16

10 Oct '16

Dear Nektar++ -Community, please can you tell me the default operator evaluation in Nektar++? In the papers "From h to p efficiently" there are mentioned three kind of types: 1. global matrix approach 2. local matrix approach 3. sum-factorization I want to choose the best hp/ configuration for my 3D simulation and this -of course- depends on the operator evaluation strategy. I think actually Nektar++ uses the global matrix approach by default, but I'm not sure by 100%. My second question depends on the error message: "Fatal : Level 0 assertion violation NaN found during time integration." While using this configuration: ======================================================================= EquationType: EulerCFE Session Name: 3Dmeshcube_h10 Spatial Dim.: 3 Max SEM Exp. Order: 3 Num. Processes: 24 Expansion Dim.: 3 Riemann Solver: HLLC Advection Type: Projection Type: Discontinuous Galerkin Diffusion Type: Advection: explicit AdvectionType: WeakDG Diffusion: explicit Time Step: 0.01 No. of Steps: 10000 Checkpoints (steps): 1000 Integration Type: RungeKutta2_ImprovedEuler Problem Type: General ======================================================================= Initial Conditions: - Field rho: rhoInf + (0.01 * exp(-0.077*(x^2 + y^2 + z^2))) - Field rhou: rhoInf * uInf - Field rhov: rhoInf * vInf - Field rhow: rhoInf * wInf - Field E: (pInf / (Gamma - 1)) + ((rhoInf/2) * uInf^2) + ((0.01/(Gamma-1))*exp(-0.077*(x^2 + y^2 + z^2))) +( (0.01/2) * uInf^2 * exp(-0.077*(x^2 + y^2 + z^2))) I already changed my time-step and the refinement of my mesh and i think this error message is because of oscillation of my solution. So maybe my mesh is not fine enough or i must increase p. But i want to use a fix h to p constellation to test the efficiency. Can anybody help me with this problem? I already tried to use the spectral hp dealiasing, the smooth advection and artificial viscosity, but it doesn't worked or helped... Thanks for any answer. Best regards Fabian

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2d axisymmetric model and LES requeriments
by Manuel F. Mejía De Alba 06 Oct '16

06 Oct '16

Dear Nektar team, I trying to model the experiment developed by HIshida 1987. (Hishida, K., Maeda, M., 1987. Turbulent characteristics of gas–solids two-phase confined jet: effect of particle density. Jpn. J. Multiphase Flow 1, 56–69.) The problem is the Re number is near to 3E4, then the model is computationally expensive. Here my questions: 1. Is it possible to developed an axisymmetric model in Nektar++ ? I found this file http://prism.ac.uk/wp-content/uploads/2014/07/gabriele2014.pdf, on this said that G. Rocco is working or worked on it. May I implement the model based on his work ? 2. For this 3D model, the mesh requirements are about 3E10, If I use a LES model with SVVCutoffRatio=0.5N and SVVDiffCoeff=0.5, how can I evaluate the new mesh requirements Thanks in advance for your comments, --- Manuel Felipe Mejía De Alba.

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Error with Hybrid Meshes
by Jian Yu 02 Oct '16

02 Oct '16

Hi everyone, I ran a 2D case with hybrid meshes(triangular and quadrilateral elements), and encountered the following error: Fatal : Level 0 assertion violation eid must be between 0 and 2 Could anyone help me figure out the problem? The xml file is attached. Thank you in advance! Best wishes Jian

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