November 2018 - Nek5000-users - mailman3.cels.anl.gov

Heat flux boundary condition
by nek5000-users＠lists.mcs.anl.gov 30 Nov '18

30 Nov '18

Hi Neks, i am calculating a laminar pipe flow. The temperature boundary conditions are a fixed fluid temperature at the entrance and a constant wall heat flux over a short section in the middle oft the pipe. The remaining pipe wall is adiabatic. For the velocity field I assume periodic BCs. Because the given heat flux contour over the axial coordinate should be an ideal hat-function, I expected the temperature gradient to have the same contour. But when calculating the temperature gradient at the wall, the resulting temperature gradient contour doesn´t represent an ideal hat-function but a more rounded down contour. Now I am wondering, if Nek can not implement the given heat flux BC correctly. Did anybody have similar experiences? Thank you! Theresa

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Mesh with a large number of curves
by nek5000-users＠lists.mcs.anl.gov 26 Nov '18

26 Nov '18

Hi, Neks! I wonder if there is any instrument to create mesh for Nek5000 with complex geometry with a large number of curves? The problem is in the fact, that typically mesh creators (like GAMBIT or PointWise) create points only for the boundaries of spectral elements, then Nek creates points according with GLL rule so that they either go beyond the boundaries of real geometry or cut it off. I want mesh points to be directly on the surface of my geometry. Best regards, Markus

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Placing cyllinder near wall
by nek5000-users＠lists.mcs.anl.gov 25 Nov '18

25 Nov '18

Hi all, I'm testing the effects of near wall obstacles, but I'm struggling to decide for a adequate method to build the mesh. The main goals are to have a hyperbolic mesh spacing perpendicularly to the the wall and easiness to place a cylinders inside that mesh close to a wall. So far I've been using makenek to build a series of boxes and replacing one with a cylinder box. The main issue is that grid size is hyperbolic everywhere, except in the boxes that lay in axis of the cylinder, where the mesh becomes uniform in order to fit the cylinder generated with makenek; and that the custom Fortran script that generates the .box files is quite bothersome to modify freely. I was wondering if nekenk could be used to place a cylinder inside a box with user-specified distribution or if you could recommend a meshing software or code that could do the job (hopefully linux-friendly and free). Regards, *Nicolás*

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Error Loading .re2 Mesh
by nek5000-users＠lists.mcs.anl.gov 19 Nov '18

19 Nov '18

Hello, I've created a mesh using Cubit 15.0 with HEX27 elements. The Jacobian for these elements are all positive and by all appearances it is a conformal mesh (no unmerged vertices, surfaces, or curves and it imports correctly in both Cubit and VisIt). I was able to convert the mesh from Exodus format (.exo) to the .re2 format using the "exo2nek" script and created a map file (.ma2) using the "genmap" script. However, when I try to use this mesh in Nek5000, it gives the following errors (found in the logfile): element load imbalance: 0 612 612 done :: mapping 0.63601 sec ERROR 2 READING MESH DATA NEAR ELEMENT 6 ABORTING IN ROUTINE RDMESH. an error occured: dying ... I cannot tell why it is crashing. My mesh is a 3D mesh with a total of 19584 elements, with all of them being flow elements. I specified in the .rea file the following: **MESH DATA** 19584 3 19584 NELT,NDIM,NELV Is this perhaps the problem? Did I not specify this line correctly? Or is something wrong with the mesh? Thanks, Matt

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How to achieve the exo format mesh with HEX20 type?
by nek5000-users＠lists.mcs.anl.gov 18 Nov '18

18 Nov '18

Dear Neks, I have seen that the tools exo2nek is proposed for mesh format conversion but I am quite wondering how I can get the .exo format mesh from ICEM. Should I directly output the unstructured mesh with the solver selected as EXODUS-II and put the .exo mesh into use for exo2nek? How can I ensure the .exo format is comprised of HEX20 meshes? Thank you so much for your comments! Haoran

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Accuracy & errors
by nek5000-users＠lists.mcs.anl.gov 15 Nov '18

15 Nov '18

Dear Nek users, I would like to do a quick test to see the difference in accuracy using two different P-orders, i.e. N = 7, and N = 11. The question I have is about the role of time integration errors. If the code uses 2nd or 3rd order of integration in time. That means that at some point the time-integration error will be larger than the spatial error. I wonder what are conditions under which it happens? Because once you are in that regime you will not see any difference between the various methods. Thanks for the help.

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Moving wall in userbc
by nek5000-users＠lists.mcs.anl.gov 15 Nov '18

15 Nov '18

Hello Neks, Since my mesh is quiet complex, it is difficult to impose velocities into the moving wall in userbc. Is there any other way to filter(highlight) the moving wall bcs from inlet bcs in userbc other than using the positions? Regards Sijo George

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Moving wall in userbc
by nek5000-users＠lists.mcs.anl.gov 15 Nov '18

15 Nov '18

Hello Neks, Since my mesh is quiet complex, it is difficult to impose velocities into the moving wall in userbc. Is there any other way to filter(highlight) the moving wall bcs from inlet bcs in userbc other than using the positions? Regards Sijo George

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Problems in getting eigenvalues using ARNOLDI
by nek5000-users＠lists.mcs.anl.gov 08 Nov '18

08 Nov '18

Hi Nek, I am running ARNOLDI simulation case for a flow over a 2D cylinder using ARPACK . My domain is [-50,50] and Re=50. I have calculated base flow using SFD method. While calculating Eigen values I have to run the restart around 16-20 times to get an eigenvalues.txt file as an output. Also the eigenvalues that are coming most of them has zero rotation i.e., they are negative real value. Suppose I want to have 30 eigenvalues as an output and I am setting Krylov subspace as 90 then I am getting around 20 of eigenvalues having zero rotation. Kindly help as I am stuck in it for long. Thanks in advance. Regards, Alok Mishra Aerospace Department IIT Kanpur

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Re: [Nek5000-users] Genmap Error?
by nek5000-users＠lists.mcs.anl.gov 08 Nov '18

08 Nov '18

The SELF-CHK failed meaning genmap thinks two element vertices of the same element are the same. Please check your mesh for invalid elements. -----Original message----- > From:nek5000-users--- via Nek5000-users <nek5000-users(a)lists.mcs.anl.gov> > Sent: Wednesday 7th November 2018 21:11 > To: nek5000-users(a)lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Genmap Error? > > What you see is not related to MAXNEL otherwise genmap would bail out with an error message. > > On 7 Nov 2018, at 19:01, nek5000-users--- via Nek5000-users <nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]>> wrote: > > Hi! > > Maybe you should increase MAXNEL parameter in maketools script (Nek5000/tools)? > > nek5000-users <nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]>>: > Hello, > I created a ".re2" mesh by converting an Exodus (".exo") mesh from Cubit > 15.0 using the "exo2nek" script. It's a relatively large mesh (780k > elements) and I need to run it using parallel processing, and so I > wanted to use the "genmap" script. > > However, I keep getting these errors, no matter what input mesh > tolerance value I use, from 0.2 to 0.00001): > > genmap > Input .rea / .re2 name: > RCF_3D_FullSimple > reading RCF_3D_FullSimple.re2 > Input mesh tolerance (default 0.2): > NOTE: smaller is better, but generous is more forgiving for bad meshes. > 0.00001 > reading mesh data ... > start locglob_lexico: 8 775728 6205824 > 1.0000000000000001E-005 > locglob: 1 1 6205824 > locglob: 2 11290 6205824 > locglob: 3 15413 6205824 > locglob: 1 632909 6205824 > locglob: 2 632909 6205824 > locglob: 3 632909 6205824 > locglob: 1 632909 6205824 > locglob: 2 632909 6205824 > locglob: 3 632909 6205824 > > 593741 2 4 Matrix: SELF!! > 1 SELF!! 313837 313837 313837 313837 > 2 SELF!! 313837 313837 313837 313837 > cont: SELF!! 593741 > > ABORT: SELF-CHK 1 2 593741 0 > Try to tighten the mesh tolerance! > > 0 quit > > > Do you have any idea what this means? Just from the output, it looks > like it's saying there are coincident vertices or elements? Is it a > problem with my mesh or with running the script? > > Thanks, > Matt > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users

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