May 2017 - Nek5000-users - mailman3.cels.anl.gov

Re: [Nek5000-users] Full restart with increasing lx ([email protected])
by nek5000-users＠lists.mcs.anl.gov 25 Jul '17

25 Jul '17

Hello, I've been able to use the full restart function increasing lx1, but in my case I had to change the timestep size (DT) in order to satisfy the CFL condition, so the solution that was saved did not work properly with the full restart because it was obtained using a different DT. So this is something for you to consider. Best, Juan Diego

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Read file without using load_fld nor mfi subroutines
by nek5000-users＠lists.mcs.anl.gov 01 Jun '17

01 Jun '17

Hi Neks, I may have a problem when I'm trying to read velocity field (only velocity field, I don't need pressure.) so I can assign specific boundary conditions using userbc(). My questions are : 1) Is it possible to read velocity fields in nek that are contained in .f000* files without modifying the pressure "pr" nor the velocity fields "vx,vy,vz" ? 2) Is there any subroutine (besides load_fld or mfi) that would allow me to read .f000* files? When I use the mfi (in ic.f) subroutine, it looks like the pressure field is modified and hence I'm quickly running into errors like the following: 100 **ERROR**: Failed in HMHOLTZ: VELX NaN NaN 1.0000E-12. If I use load_fld() I seem to me going back to the initial conditions. Thank you for your help, Arnold

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Streamwise velocity and vorticity
by nek5000-users＠lists.mcs.anl.gov 31 May '17

31 May '17

Hi nek, Is there any example using nek5000 to simulate a pipe flow. I want to output the streamwise velocity and vorticity, but I don't know how to write in usr file. Kind regards, Jian

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Full restart with increasing lx
by nek5000-users＠lists.mcs.anl.gov 23 May '17

23 May '17

Hello Neks, Can restart a simulation by my_full_restart and also increase the lx in the SIZE file? Thank you in advance. Sincerely, Sandeep

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Re: [Nek5000-users] Contents of Nek5000-users digest, Vol 99, Issue 14 Message 1
by nek5000-users＠lists.mcs.anl.gov 22 May '17

22 May '17

Hi Paul, thank you very much for your quick and detailed answer. I have might ask you two follow up questions. 1) Is the following statement correct? In order to compare my energy spectrum with literature values, I therefore have to use pi/2 times more points to have an identical kmax. 2) Not really in the same context, but why is the energy spectrum of "coarse DNS" almost identical to a fully resolved DNS? Are Pope's resolution recommendations too conservative for NEK, so that the Kolmogorov scales can be captured with significant less points or are there some routines in the background that prevent a growing instability in the high modes, if the dissipation regime is under resolved? Thanks, Daniel

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Compilation problem on Blue Gene
by nek5000-users＠lists.mcs.anl.gov 22 May '17

22 May '17

Hi Neks, I am facing a compilation problem on Blue Gene machine. I get the following message towards the end: I am attaching the makenek file that I am using for compilation. ld: skipping incompatible $HOME/NEK_2017/3rd_party/gslib/src/libgs.a when searching for -lgs ld: cannot find -lgs Thanks, NN.

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velocity averaging code in .usr file for a pipe
by nek5000-users＠lists.mcs.anl.gov 21 May '17

21 May '17

Hi nek, Are there any examples of averaging velocity for fluid and particles (if it is a two-phase flow) in a pipe in .usr file? Kind regards, Jian

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Low Mach configuration in Nek5000
by nek5000-users＠lists.mcs.anl.gov 20 May '17

20 May '17

Hello, I am trying to simulate two membranes that produce a synthetic jet with Nek5000. I have been using the low Mach configuration in Nek5000 (the flow conditions are low Mach). The low Mach set up in the low_mach example was helpful but I still have a few questions: - the low Mach does not seem to work for PnPn-2 formulation. Following this remark, what would be the correct set up with the low Mach approach to compute the full stress tensor with variable viscosity? - the user manual reads 'The implementation of the equation if state for the Low Mach formulation is for the moment hard-coded to be the ideal gas equation of state p = ρRT. This allows for both variable density and variable viscosity.’ Does that mean the density is always computed using the ideal gas equation of state? What does happen when the density is specified in uservp? - since I have a moving boundary condition ‘mv’ and I solve the heat equation, what would be a good boundary condition for the temperature at the membranes? I do not think ‘mv’ boundary type is supported for the heat equation. I have tried with ’t’ and ‘I’ without noticing any significant differences in the numerical solution. Thanks, Marco

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Resolution problems at computation of the energy spectrum
by nek5000-users＠lists.mcs.anl.gov 19 May '17

19 May '17

Hi Neks, I am currently performing DNS of a 3d periodic box. It seems I might have encountered a resolution problem while working on the spectral analysis of the velocity field. In short: The high wavenumber modes appear to be insufficiently resolved by the GLL points / polynomials causing effects similar to aliasing and therefore a significant distortion of the energy spectrum, which can also be observed away from the high wavenumber end. The comparison of my energy spectra with literature values revealed that the energy in the high wavenumber end is significantly underestimated. In order to make sure that this deviation is not caused by a bug in my post processing, I bypassed the routine by analyzing the NEK output of a simple test case in MATLAB. In this simple 3d 2pi box the velocity is initialized as vx=sin(30*x), vy=vz=0.0 on a grid with N=65 (nelx=8,lx1=9). The regular grid output (ifreguo=.true.) of this initial time step (zeroth time step - no equations were solved) was compared to sin(30*x). Here is a plot of this comparison http://imgur.com/a/2c1q5. The deviations lead to a redistribution of the energy among several modes. Currently I am wondering if there is any solution which allows for a computation of a less distorted energy spectrum without increasing the number of elements or polynomial order, and to subsequently cutting off the high modes. I already increased the number of equidistant grid points by increasing lxo to 1.5*lx1, however the quality of the energy spectrum is not improved as the interpolation deviates nonetheless. I am looking forward to helpful suggestions or an interesting discussion, Daniel

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Problem in using .re2 file
by nek5000-users＠lists.mcs.anl.gov 19 May '17

19 May '17

Hi Neks, I have encountered a problem while using .re2 file. When I use it, I get the following warning in the output file and the code hangs up. WARNINGb: Detected non-right-handed element. Number 14621 V1-8: -.1290E+21 .0000E+00 .6991E+01 .0000E+00 WARNINGb: Detected non-right-handed element. WARNINGb: Detected non-right-handed element. If, however, I use the full ASCII .rea file, the code runs fine. What could be the problem in using .re2 file? Kindly suggest a remedy. I would like to mention that first I create the full ASCII .rea file and generate the .map file from it. Then, I use the executable "reatore2" to make the .re2 file and smaller ASCII .rea file. I do not make any change in the smaller ASCII .rea file. Many thanks, NN.

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