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

Сollocation of i,j,k in each spectral element
by nek5000-users＠lists.mcs.anl.gov 11 Jan '18

11 Jan '18

Hi, Neks! I am working with a complex geometry witch was built in gambit. And I want to change positions of some points in spectral elements. I've read in documentation that i,j,k,e in xm1(i,j,k,e), for example, are changed from 1 to nx1,ny1,nz1 and nelv respectively. But during my tests it's seemed that in different elements x,y,z axis not always correspond to the global coordinate system. Am I right? And how could I find out the principle of collocation of i,j,k in each spectral element? Best regards, Elizabeth

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Question about iside value
by nek5000-users＠lists.mcs.anl.gov 11 Jan '18

11 Jan '18

Hi, Neks! I am working with a complex geometry witch was built in gambit. I want to know a parameter "iside" for each of faces ( outflow, inflow and all walls) on zero step. If I ask in userbc ( in *.usr file) write "iside", I receive only iside=1, that matches inflow. It means that faces with type "wall" don't have "iside" value,am i right? And how each surface is assigned value "iside"? Best regards, Elizabeth

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Re: [Nek5000-users] Nek5000-users Digest, Vol 105, Issue 32
by nek5000-users＠lists.mcs.anl.gov 30 Nov '17

30 Nov '17

Dear Ketan, Many thanks for your reply. Basically I want to get the averaged velocity, rms velocities and shear stress where I got two questions. 1. Once the subroutines were writen in usr file, Is calling avg_all still needed? In other words, the post-processing is done after longtime running, and usr file is changed instead of calling avg_all, isn't it? 2. After trying the subroutines you provided, there isnt no files generated in the directory. Can you give me more infomation about the averaging process. Best wishes, ZJ On 30 November 2017 at 18:00, <nek5000-users-request(a)lists.mcs.anl.gov> wrote: > 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. tools in new version (nek5000-users(a)lists.mcs.anl.gov) > 2. Re: avg_all averaging (nek5000-users(a)lists.mcs.anl.gov) > 3. Re: tools in new version (nek5000-users(a)lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 30 Nov 2017 06:26:10 +0300 > From: nek5000-users(a)lists.mcs.anl.gov > To: nek5000-users(a)lists.mcs.anl.gov > Subject: [Nek5000-users] tools in new version > Message-ID: > <mailman.3666.1512012374.19102.nek5000-users(a)lists.mcs.anl.gov> > Content-Type: text/plain; charset="utf-8" > > Hi, Neks! > > I am trying to create a complex geometry and use nektools. I use nekmerge2 > script to merge two parts of my mesh, and then I want to use reatore2 and > genmap. In previous version the same script worked find, but now > (~/Nek5000/bin/) reatore2 gives a note:? > > Note: The following floating-point exceptions are signalling: > IEEE_INVALID_FLAG IEEE_DENORMAL > > and after that genmap gives a error: > > ABORT: SELF-CHK 1 2 4 0 > Try to tighten the mesh tolerance! > > I have tested this script with old tools (on another computer) and it's > still works fine. Do you have any ideas why does this problem occur? > > Best regards, > Mark > > > >

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tools in new version
by nek5000-users＠lists.mcs.anl.gov 30 Nov '17

30 Nov '17

Hi, Neks! I am trying to create a complex geometry and use nektools. I use nekmerge2 script to merge two parts of my mesh, and then I want to use reatore2 and genmap. In previous version the same script worked find, but now (~/Nek5000/bin/) reatore2 gives a note: Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG IEEE_DENORMAL and after that genmap gives a error: ABORT: SELF-CHK 1 2 4 0 Try to tighten the mesh tolerance! I have tested this script with old tools (on another computer) and it's still works fine. Do you have any ideas why does this problem occur? Best regards, Mark

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Re: [Nek5000-users] avg_all averaging
by nek5000-users＠lists.mcs.anl.gov 29 Nov '17

29 Nov '17

Hi ZJ, A quick search of the archives with keyword “avg_all” will give you answer to related questions: https://lists.mcs.anl.gov/mailman/mmsearch/nek5000-users?config=nek5000-use… avg_all is a collection of time-averaged information in the avg, rms and rm2 files. The avg files has time-averaged u,v and w; rms has time-averaged u^2, v^2 and w^2; and rm2 has uv, vw, and uw. The avg_all routines is located in navier5.f in case you want to get more information. Typically the first step in post processing is to use the routine “auto_averager” to combine all the files output from avg_all. autoaverager takes as input the name of a file (example: fname1.list) which has a list of all the files that you want to combine (example: the contents of fname1.list will be: avgcasename0.f00001 avgcasename0.f00002 … Note- there should be only 1 filename per line in the fname1.list file). You can use the auto_averager routine to combine all your avgcasename0.f00* files and output them to a single file or do more post-processing with it. The quantities available in avg, rms and rm2 files are sufficient to get the actual urms, vrms velocities etc… Additionally, once you time-average the data using auto_averager, you can use space averaging routines such as z_avg etc… to average quantities in homogeneous direction of your domain. It would also help if you specify what exactly are you trying to get from these avg_all files i.e. are you looking for rms velocities or something else? Here is a snippet of my code that I have used in the past to post-process these files: call auto_averager(fname1) call copy(uk,vx) call copy(vk,vy) call copy(wk,vz) call col2(uk,uk,lt) call col2(vk,vk,lt) call col2(wk,wk,lt) call auto_averager(fname2) call sub2(vx,uk,lt) call sub2(vy,vk,lt) call sub2(vz,wk,lt) call z_avg(vxa,vx,gs_avg_hndl,nelxy,ifld) call z_avg(vya,vy,gs_avg_hndl,nelxy,ifld) call z_avg(vza,vz,gs_avg_hndl,nelxy,ifld) call outpost(vxa,vya,vza,vxa,vya,' ') Here fname1 has the list of all avgcasename0.f00* files and fname2 has the list of all the rmscasename0.f00* files. Ketan

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avg_all averaging
by nek5000-users＠lists.mcs.anl.gov 29 Nov '17

29 Nov '17

Hi nek, May I know how I can use the files generated by calling avg_all subroutine in userchk to get the averaged velocities? Bascially, I want to have some plot some lines. Kind regards, ZJ

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Failing to converge when running in parallel
by nek5000-users＠lists.mcs.anl.gov 29 Nov '17

29 Nov '17

When running with mpi, I am currently experiencing an error with helmholtz which causes the solution to blow up quickly. The issue seems to disappear when running on lower mpi ranks. Is there a known issue which may cause this, or a work around I can employ? I haven't seen this before for similar mesh sizes. This case is a small mesh, but I plan on upscaling quite a bit. See attached for the run log and user file. Thanks, Jefferson Davis

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Conjugate Problem
by nek5000-users＠lists.mcs.anl.gov 29 Nov '17

29 Nov '17

Hello Neks, I am working on a conjugate problem with Nek5000. Is there any reference that discusses how nek5000 solves the conjugate heat transfer problem? Thanks. Mu Xu

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Nek5000 Low Mach Jet Flow
by nek5000-users＠lists.mcs.anl.gov 28 Nov '17

28 Nov '17

Hello Sir, Need to solve Low Mach number Helium (or Hydrogen ) jet opening to atmospheric air. Need to solve the species diffusion equation for this. Is it possible to solve using Nek5000? If yes,how? Thank you in advance -- Nitish Kovalam Aerospace Engineering Indian Institute of Space Science and Technology

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All elements deformed :: regenerate geometry data
by nek5000-users＠lists.mcs.anl.gov 28 Nov '17

28 Nov '17

Hi, I have prepared a 3D mesh in GAMBIT and used the matlab converter to make the .rea and .map file. When I use these files for computation, things appear to go on nicely and the flow field that I get is not different from what I expect. However, I notice the following lines in the output file which says that the geometry has been regenerated. What does this mean? Would it comprise the quality of the mesh near the wall? Reading checkpoint data byte swap: F 6.543210 -2.9312772E+35 FILE: restart.f00001 0 2.7300E+02 done :: Read checkpoint data avg data-throughput = 137.8MBps io-nodes = 1736 xyz min -3.5000 0.0000 -10.000 uvwpt min -1.5151 -1.7105 -1.6631 -0.87366 0.0000 PS min 0.0000 0.99000E+22 xyz max 60.000 3.1200 10.000 uvwpt max 2.2376 0.91592 1.7789 0.47959 0.0000 PS max 0.0000 -0.99000E+22 Restart: recompute geom. factors. regenerate geometry data 1 NOTE: All elements deformed , param(59) ^=0 done :: regenerate geometry data 1 done :: set initial conditions call userchk Many thanks, NN.

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