May 2013 - Nek5000-users - mailman3.cels.anl.gov

Re: [Nek5000-users] Vorticity
by nek5000-users＠lists.mcs.anl.gov 11 Oct '16

11 Oct '16

Hi, Thanks for your quick reply. Just I wanna know if I can use the interpolated values of velocity at some arbitrary points in the domain (not necessarily the grid points) as the input arguments to theses subroutines. Regards, Alireza Quoting nek5000-users-request(a)lists.mcs.anl.gov: > 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. Vorticity (nek5000-users(a)lists.mcs.anl.gov) > 2. Re: Vorticity (nek5000-users(a)lists.mcs.anl.gov) > 3. Re: Vorticity (nek5000-users(a)lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 13 Jul 2011 17:55:35 -0400 > From: nek5000-users(a)lists.mcs.anl.gov > Subject: [Nek5000-users] Vorticity > To: nek5000-users(a)lists.mcs.anl.gov > Message-ID: <20110713175535.1042430oct81vz2v(a)webmail.vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > Hi, > > I need to calculate the vorticity vector and the rate of strain tensor > at any arbitrary point in the domain. I wonder if these values are > computed somewhere in the code or if I should interpolate them in the > usr file. I appreciate any kind of help. > > Thanks in advance, > > > Regards, > Alireza Karimi > > > > ------------------------------ > > Message: 2 > Date: Wed, 13 Jul 2011 17:09:48 -0500 (CDT) > From: nek5000-users(a)lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Vorticity > To: nek5000-users(a)lists.mcs.anl.gov > Message-ID: <Pine.LNX.4.64.1107131704140.26989(a)jacobi.mcs.anl.gov> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > Hi Alireza, > > For vorticity computation, you can call > > call comp_vort3(vort,work1,work2,vx,vy,vz) > > from userchk with the appropriate definitions of vorticity and work arrays > like > > common /scren/ vort (lx1,ly1,lz1,lelv,3) ! x y z components > $ , work1(lx1,ly1,lz1,lelv) > $ , work2(lx1,ly1,lz1,lelv) > > Let me check what we have for the calculation of strain tensor. > Best, > Aleks > > > On Wed, 13 Jul 2011, nek5000-users(a)lists.mcs.anl.gov wrote: > >> Hi, >> >> I need to calculate the vorticity vector and the rate of strain >> tensor at any >> arbitrary point in the domain. I wonder if these values are computed >> somewhere in the code or if I should interpolate them in the usr file. I >> appreciate any kind of help. >> >> Thanks in advance, >> >> >> Regards, >> Alireza Karimi >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users(a)lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > ------------------------------ > > Message: 3 > Date: Wed, 13 Jul 2011 23:59:08 -0500 (CDT) > From: nek5000-users(a)lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Vorticity > To: nek5000-users(a)lists.mcs.anl.gov > Message-ID: > <600285192.94128.1310619548370.JavaMail.root(a)zimbra.anl.gov> > Content-Type: text/plain; charset=utf-8 > > Hi Alireza, > > > For a strain stress computation you can call subroutine comp_sij > > call comp_sij(sij,nij,vx,vy,vz > $ ,ur,us,ut,vr,vs,vt,wr,ws,wt) > > > (navier5.f:2225) with nij=6 for 3D somewhere from userchk once you > declare the stress component array sij and arrays with local > coordinate r-s-t derivatives of velocity components > > common /csij/ > $ sij(lx1*ly1*lz1,6,lelv) ! 6 components > $ ,ur (lx1*ly1*lz1) > ... > $ ,wt (lx1*ly1*lz1) > > > Best, > Aleks > > > > > > > ----- Original Message ----- > From: nek5000-users(a)lists.mcs.anl.gov > To: nek5000-users(a)lists.mcs.anl.gov > Sent: Wednesday, July 13, 2011 5:09:48 PM > Subject: Re: [Nek5000-users] Vorticity > > Hi Alireza, > > For vorticity computation, you can call > > call comp_vort3(vort,work1,work2,vx,vy,vz) > > from userchk with the appropriate definitions of vorticity and work arrays > like > > common /scren/ vort (lx1,ly1,lz1,lelv,3) ! x y z components > $ , work1(lx1,ly1,lz1,lelv) > $ , work2(lx1,ly1,lz1,lelv) > > Let me check what we have for the calculation of strain tensor. > Best, > Aleks > > > On Wed, 13 Jul 2011, nek5000-users(a)lists.mcs.anl.gov wrote: > >> Hi, >> >> I need to calculate the vorticity vector and the rate of strain >> tensor at any >> arbitrary point in the domain. I wonder if these values are computed >> somewhere in the code or if I should interpolate them in the usr file. I >> appreciate any kind of help. >> >> Thanks in advance, >> >> >> Regards, >> Alireza Karimi >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users(a)lists.mcs.anl.gov >> 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 > > > ------------------------------ > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > End of Nek5000-users Digest, Vol 29, Issue 2 > ******************************************** > -- Alireza Karimi PhD Candidate Department of Engineering Science and Mechanics Virginia Polytechnic Institute and State University Blacksburg, VA 24061

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Error in generalev
by nek5000-users＠lists.mcs.anl.gov 02 Jul '14

02 Jul '14

Hello Neks, I've recently come across an error I haven't seen before. It occurs in the routine "generalev" at the beginning of my run. It looks like the matrix "a" and "b" being fed to the routine have an Infinity or NaN at position (0,0). Are there any ideas of what could cause this type of error? I have attached the logfile to this email. Thanks, -- Josh Camp "All that is necessary for the triumph of evil is that good men do nothing" -- Edmund Burke

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Linearized Nek: Compute only the right-hand side
by nek5000-users＠lists.mcs.anl.gov 21 Jan '14

21 Jan '14

Hi Nek's, Given a random initial vector u and the Jacobian matrix of the linearized Navier-Stokes, I would like to calculate the matrix-vector product J * u. In Nek, that would consists in calculating only the right hand side of the equations, that is: RHS = ( -U.grad(u) - u.grad(U) - grad(p) + 1/Re Lap(u) ; div(u) ) I have a few questions on how to compute those different terms in userchk (Nek is used in post-process mode): - I would tend to use convop() for the convection terms, however I'm not sure whereas it would output the strong or weak form (and I need the strong one obviously)? - Same question regarding grad(p) and div(u) if I use opgradt() and opdiv() to calculate them? Last but not least, for the Laplacian I've read a previous mail where it is said that it can be computed using a sequence of wgradm1() and vec_dssum() so I guess I kown how to compute at the strong form for it. Sincerely, -- Jean-Christophe

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neuman bc for the normal velocity component
by nek5000-users＠lists.mcs.anl.gov 23 Oct '13

23 Oct '13

Dear Nekians, I'm relatively new to nek. I would like to compute the flow of a boundary layer and I would like to impose the following boundary condition on the top (2D) boundary, which is parallel to the wall: u = U_base and dv/dy = - dU_base/dx, where U_base is the known inviscid base flow. The velocity component u is parallel to the boundary, whereas v is normal. I tried to use 'ON ' but this did not give the result I was expecting (Am I doing smth. wrong?). At the boundary nodes u was equal to U_base, but at the very next node u was completly different (and v was of course completly wrong). Thanks for any help Joris

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Compilation Error on BG/Q
by nek5000-users＠lists.mcs.anl.gov 15 Oct '13

15 Oct '13

Hi neks! On the BG/Q in Jï¿½lich we encounter several errors while compiling nek5000 (Revision: 853). Please find attached the compiler output, the makenek script and the makefile. The installed compiler versions are "IBM XL C/C++ for Blue Gene, V12.1" and "IBM XL Fortran for Blue Gene, V14.1". Did you come across similar problems on your BG/Q runs? Do you have any hint how I can fix this? Thanks in advance Fabian

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problem with closed internal boundaries
by nek5000-users＠lists.mcs.anl.gov 23 Jul '13

23 Jul '13

Hello Neks, I'm trying to model a flow past an obstacle in a channel. As a first step I would like to do a 2D simulation. I'm encountering some problems during the geometry data generation in the nek5000 execution : it looks like the program can only generate NaN values although genmap seems to work well on the .rea file. I can also reopen the rea file with prenek without any problems. Do you have any idea what is going wrong here? Is it problematic to have a closed internal boundary condition? Thanks in advance for any help. Best, Michael B

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Re: [Nek5000-users] Prenek and Genbox - Maketools problems
by nek5000-users＠lists.mcs.anl.gov 04 Jun '13

04 Jun '13

Hi Katie, Thanks, genbox is creating the .re2 file without any errors now and you are right regrading the IO error.. it appears since I close prex by just closing the window. Regarding what's happening with PRENEK: in general, for 'PREX', it prints the following error every time when opening: 'I/O Error: No String Terminator sent to PRS' Then when I input a name for the session (after the prompt "Choose a Name for This Session:" ) the program does nothing. It doesn't take the session name and I can keep on typing text and pressing enter with no response. On the other hand, for 'PRETEX', it doesn't show the 'I/O Error: No String Terminator sent to PRS' at the beginning but gives: 'cp: cannot stat `/home/jpm/.nekdefaults': No such file or directory' It lets me input a session name and this time it accepts it and i manage to go through the menu options but when trying to 'read previous parameters' it gives 'Error reading parameters from file.' When I try the 'Type in new parameters' it lets me carry on but when I try to 'Build interactively' the following message appears: 'Error: Grid must be between 0 and 1 (fraction of Screen height). Screen gridding couldnt be changed drwobjs: 0' I then go through some stages, and manage to, for example, use the 'Import Mesh' but the mesh is not imported correctly and grey boxes appear (which I imagine should be clickable options) but there is nothing inside them. Other options seem to work partially but never successfully, it is as though there is something wrong with the output to the Nekton window. Sorry if the above is confusing but I tried to summarise what is happening. Thank you, JP

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Re: [Nek5000-users] Prenek and Genbox - Maketools problems
by nek5000-users＠lists.mcs.anl.gov 24 May '13

24 May '13

Hi Katie, Yes thanks, the problem when compiling is solved. I imagined it was something related to bash but it didn't cross my mind to check the makefile. Unfortunately the errors with genbox (when trying to output a .re2 file) and prex (the errors I mentioned + interface does not work well) still remain (even after re-making the tools). Thanks, JP

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trouble with visit
by nek5000-users＠lists.mcs.anl.gov 24 May '13

24 May '13

Hi Neks, I am facing problems with the visualization in visit. The output of the three scalar fields uzt, epst, epsv is done is seen in the following line from my usr file. Here, I wrote the data into four files (see further below). I also attach the visit script !-------usr file------------------------------------------------- tiny=1.e-16 do i=1,n epst(i)=log(epst(i)+tiny) epsv(i)=log(epsv(i)+tiny) enddo !-------No pressure field, no scalar output ifpo=.false. ifto=.false. call outpost2( uzt,epst,epsv,pr,t,0,'eps') ifpo=.true. ifto=.true. !-------Visit script------------------------------------------------ NEK5000 version: 1.0 filetemplate: epsG1_64%d.f%05d firsttimestep: 1 numtimesteps: 1 !-------the four files that have to be load into visit and which make up one snapshot-------------- -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:03 epsG1_640.f00001 -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:09 epsG1_641.f00001 -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:16 epsG1_642.f00001 -rw-r--r-- 1 josc1234 linux 2657536136 27. Feb 08:22 epsG1_643.f00001 -rw-r----- 1 josc1234 linux 87 20. Mär 13:37 vis.nek5000 !-------This is the error message in visit--------------------------------------- The compute engine running on makalu51.rz.tu-ilmenau.de has exited abnormally. Shortly thereafter, the following occured... The Pseudocolor plot of "y_velocity" for the file "/usr/wrk/people4/josc1234/nek5_visit/r095_Lx1_12_Ra1e8/vis.nek5000" could not be generated by the compute engine on host "localhost". My questions: Could it be that the graphics output should be in single precision? I saw that the people at KTH did have similar trouble. If yes, how can I switch to single precision in the usr file output? For smaller grid it worked. Thanks in advance, Joerg.

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Problem reading restart data
by nek5000-users＠lists.mcs.anl.gov 24 May '13

24 May '13

Hello Neks. We just got a new system and I'm trying to run some nek cases that worked fine on our previous systems. Everything seems fine when running without having to read initial condition data. However, I'm having a problem reading in restart data, e.g., from the log file: " Error reading initial condition/drive force data aborting in routine rdicdf. EXIT: rdicdf error 1 call exitt: dying … " Our new system has the Xeon E5-2670 "SandyBridge" cores and FDR (Fourteen Data Rate, or 56 Gb/sec) InfiniBand Our old system Intel Nehalem processors and InfiniBand interconnect Here's the mpi info on the new system.: login4 >> mpif77 -v mpif77 for the Intel(R) MPI Library 4.1 for Linux* Copyright(C) 2003-2012, Intel Corporation. All rights reserved. ifort version 13.0.1 Any ideas why I'm having trouble reading in restart data on this new system? Thanks! --Mike

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