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

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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gradient at every point
by nek5000-users＠lists.mcs.anl.gov 07 Nov '18

07 Nov '18

Hi, I am a new user. Want to calculate gradient at every point so as to obtain TKE values. Is there a subroutine for this? Thanks, Samuel

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Genmap Error?
by nek5000-users＠lists.mcs.anl.gov 07 Nov '18

07 Nov '18

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

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Remesh a moving geometry
by nek5000-users＠lists.mcs.anl.gov 07 Nov '18

07 Nov '18

Hi Neks We try to simulate a flow with a moving geometry. In order to avoid large geometry distortions, we have to remesh the geometry at regular intervals. It is possible to remesh the geometry during a simulation without a restart? Best regards, Philipp

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'COMMON' block issue
by nek5000-users＠lists.mcs.anl.gov 07 Nov '18

07 Nov '18

Dear Nek users, Currently, I am working on a simulation with a decent size (11760 * 12 elements) employing ‘lpmin = 32’. When I compile, I received an error saying: “relocation overflows omitted from the output”. I googled this error and it turned out this error comes from the ‘COMMON’ block; Static data, such as COMMON variables, and all of the code together is still limited to 2GB under any mcmodel. The suggested solution is to move the data out of a COMMON block and into a module and make the data allocatable. The most straightforward way to avoid this would be increase the ‘lpmin’ (for example if lpmin = 64, then it works), but this does not solve this issue, which is a big constraint. I am wondering has anyone has run into this and got any experience in solving it? Thanks a lot in advance

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Variable properties and Reynolds number
by nek5000-users＠lists.mcs.anl.gov 31 Oct '18

31 Oct '18

Hi, Neks! I have a question about setting Reynolds number and using variable properties in uservp (density, viscousity and etc.). I want to solve an dimensionless equation (1D case, for example): rho*Cp*(dT/dt + ux*(dT/dx))=(1/Pe)*d(k(dT/dx))/dx, where rho*Cp I set in uservp (utrans for ifield = 2) and it's variable, k I set in uservp (udiff for ifield = 2) and it's variable. According to the documentation for using uservp I must use "variableProperties = yes" in .par file, and for the Peclet number I must use "conductivity = -3536.69" (minus for Pe), but I was looking at the code and noticed that both of "uservp" and "conductivity" use vtrans array. Does it mean that in case of variable properties I could solve only rho*Cp*(dT/dt + ux*(dT/dx))=d(k(dT/dx))/dx, without my Peclet number and I sould to include it in uservp in k, for example? Best regards, John.

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Different P-order across domain
by nek5000-users＠lists.mcs.anl.gov 23 Oct '18

23 Oct '18

Dear Nek users I have two quick questions: Q1) Is it possible to change the order of polynomial for different sections of the geometry? For example a pipe with an expansion in the downstream. _______________ /| | | / | | | /| | | | ________________/ | | | | | | | | | | | | | | | | | | | | +-----+-----+---+--+---+------+------+----> z <--- Pn=6 --><------ Pn=8 -----------> Q2)Would it be feasible to restart using a different P-order? Thanks for the help in advance

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Re: [Nek5000-users] Sub-grid turbulent kinetic energy
by nek5000-users＠lists.mcs.anl.gov 19 Oct '18

19 Oct '18

I'm currently using the hpfrt model but am planning to try out a couple (such as dynamic Smagorinsky) in the future. Cheers, Daniel ________________________________ From: Nek5000-users <nek5000-users-bounces(a)lists.mcs.anl.gov> on behalf of nek5000-users-request(a)lists.mcs.anl.gov <nek5000-users-request(a)lists.mcs.anl.gov> Sent: 10 October 2018 18:00 To: nek5000-users(a)lists.mcs.anl.gov Subject: Nek5000-users Digest, Vol 116, Issue 6 Send Nek5000-users mailing list submissions to nek5000-users(a)lists.mcs.anl.gov To subscribe or unsubscribe via the World Wide Web, visit https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users or, via email, send a message with subject or body 'help' to nek5000-users-request(a)lists.mcs.anl.gov You can reach the person managing the list at nek5000-users-owner(a)lists.mcs.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Nek5000-users digest..." Today's Topics: 1. Sub-grid turbulent kinetic energy (nek5000-users(a)lists.mcs.anl.gov) 2. Re: Sub-grid turbulent kinetic energy (nek5000-users(a)lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Wed, 10 Oct 2018 14:39:47 +0000 From: nek5000-users(a)lists.mcs.anl.gov To: "nek5000-users(a)lists.mcs.anl.gov" <nek5000-users(a)lists.mcs.anl.gov> Subject: [Nek5000-users] Sub-grid turbulent kinetic energy Message-ID: <mailman.12319.1539182408.86639.nek5000-users(a)lists.mcs.anl.gov> Content-Type: text/plain; charset="iso-8859-1" Hi, I'm trying to compute the efficacy of my LES and would like to do this by considering the ratio of turbulence kinetic energy both on the grid and sub-grid. Is there an option within NEK (maybe in .par) to include the amount of sub-grid TKE as an output from the simulation itself, so that I can directly compare it to the computed on-grid TKE? Cheers, Daniel Ward

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Boundary nodes cordinates and random generator
by nek5000-users＠lists.mcs.anl.gov 16 Oct '18

16 Oct '18

Hello Neks, Its been a long time that I posted something in NEK5000. Here I came up with something which is simple. First thing is, I was trying to access the co ordinates of the inlet boundary elements for my free stream turbulence model(Von karman). I have an idea to get the using cbc(f,e,1) but I just would like to know is there any quick way to get the inlet bounday nodes coordinate. Second thing is about the making of random numbers. I know that in fortran there is an inbuilt function to generate random numbers (call random_generator(iseed)) but it seems it is an expensive process since my number of modes of turbulence model is 150. So just I have a question that how you usually generate random numbers when you model free stream turbulence? By the way I have completed the FSI calculation of NACA0012 at Re 64000 in NEK5000. Thanks for your help. Regards Sijo GEORGE

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Rotating computational domain
by nek5000-users＠lists.mcs.anl.gov 13 Oct '18

13 Oct '18

Hello Neks, I am an undergraduate student new to Nek and I am working on a simulation studying dynamic stall in a dynamically pitching airfoil. I want to do a pitch and hold simulation at low Reynold's number (Re = 12000) where I rotate the entire computational domain up to about 50 degrees AOA and then hold at 50 degrees, with steady inflow ux = 1. I would like to rotate the domain about the z axis, which passes through the quarter chord location of the airfoil profile (modified NACA 0012). Because of the steep AOA, I would like to stay away from pitching the airfoil within the stationary domain with ALE to avoid too much mesh deformation. To this end, I have been scouring documentation to try and find a method of applying a rotational mesh velocity to the entire domain about the z axis while keeping the flow within the domain at ux = 1. I am feeling very stuck. Others have suggested applying a Coriolis force to the flow, but I don't really see how this would simulate rotation of the entire domain. It seems to me that simulation of a Coriolis force would be acceptable to correct the flow field to always be ux = 1 inside a rotating domain, but I don't see how that would apply a mesh velocity anywhere. Are there any examples where an entire computational domain is rotated that I can look at, or has anybody done similar work who can point me in the right direction? Regards, -Harry

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