March 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

1 3

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

1 11

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

1 4

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

1 4

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

1 5

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

1 9

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.

1 13

postnek on a mac
by nek5000-users＠lists.mcs.anl.gov 16 Apr '13

16 Apr '13

Hello all, I have downloaded the most recent version of the software and am trying to compile postnek on a mac running lion with gfortran and gcc. The command: ./maketools postnek Gives the following error: Warning: Deleted feature: ASSIGN statement at (1) gcc -mcmodel=medium -c -O2 xdriver.c xdriver.c: In function ‘TypeChar’: xdriver.c:1790: warning: comparison is always true due to limited range of data type xdriver.c: In function ‘error’: xdriver.c:1910: warning: format not a string literal and no format arguments xdriver.c:1910: warning: format not a string literal and no format arguments gfortran -mcmodel=medium -c scrdmp.f gfortran -mcmodel=medium -c coef.f gfortran -mcmodel=medium -c postnek7.f gfortran -mcmodel=medium -c speclib.f gfortran -mcmodel=medium -c mxm.f gcc -mcmodel=medium -c -DUNDERSCORE ../../nek/byte.c gfortran -mcmodel=medium -c ssyev.f gfortran -mcmodel=medium -c iolib.f gfortran -mcmodel=medium -o /Users/mrp/bin/postx postnek.o postnek2.o postnek3.o postnek5.o postnek6.o tsort.o postnek8.o postnek9.o plot.o getfld.o legend.o userf.o revert.o trap.o animate.o genxyz.o screen.o g3d.o subs.o xinterface.o locglob.o postnek5a.o blas.o xdriver.o scrdmp.o coef.o postnek7.o speclib.o mxm.o byte.o ssyev.o iolib.o -L/usr/X11R6/lib -lX11 -lm ld: in xdriver.o, in section __TEXT,__text reloc 3: length != 2 and X86_64_RELOC_GOT not supported for architecture x86_64 collect2: ld returned 1 exit status make[1]: *** [postx] Error 1 make: *** [all] Error 1 Any ideas? Thanks, Mark

1 5

Download and running of nek5000
by nek5000-users＠lists.mcs.anl.gov 27 Mar '13

27 Mar '13

Dear sir , I am a new mac user . I am trying to download the Nek5000 software but my MacBook Pro is telling me "Checked out revision 906 " . Later when I try to implement the different commands needed for the initial build I have lots of comment like "command not found" or " *** No rule to make target " and so on . This is what I have from my terminal : "Last login: Mon Mar 25 12:47:38 on ttys000 dhcp168:~ giacintogenco$ sudo svn co https://svn.mcs.anl.gov/repos/nek5/ svn: OPTIONS of 'https://svn.mcs.anl.gov/repos/nek5': Could not resolve hostname `svn.mcs.anl.gov': Host not found (https://svn.mcs.anl.gov) dhcp168:~ giacintogenco$ ~/nek5_svn/trunk/tools/maketools clean make: *** No rule to make target `clean'. Stop. dhcp168:~ giacintogenco$ ~/nek5_svn/trunk/tools/maketools all make: *** No targets specified and no makefile found. Stop. dhcp168:~ giacintogenco$ make -f <filename of makefile> -bash: syntax error near unexpected token `newline' dhcp168:~ giacintogenco$ svn co https://svn.mcs.anl.gov/repos/nek5/ nek5_svn Checked out revision 906. dhcp168:~ giacintogenco$ ~/nek_svn/trunk/tools/maketools -bash: /Users/giacintogenco/nek_svn/trunk/tools/maketools: No such file or directory dhcp168:~ giacintogenco$ sudo svn co https://svn.mcs.anl.gov/repos/nek5/ Password: Sorry, try again. Password: Checked out revision 906. dhcp168:~ giacintogenco$ nek5_svn/trunk/tools/maketools Usage: maketools [clean|all|tool(s)] dhcp168:~ giacintogenco$ nek5_svn/trunk/postnek/makefile -bash: nek5_svn/trunk/postnek/makefile: No such file or directory dhcp168:~ giacintogenco$ svn co https://svn.mcs.anl.gov/repos/nek5/ nek5_svn Checked out revision 906. dhcp168:~ giacintogenco$ nek5_svn/trunk/postnek/makefile -bash: nek5_svn/trunk/postnek/makefile: No such file or directory dhcp168:~ giacintogenco$ nek5_svn/trunk/tools/maketools Usage: maketools [clean|all|tool(s)] dhcp168:~ giacintogenco$ maketools all -bash: maketools: command not found dhcp168:~ giacintogenco$ maketools clean -bash: maketools: command not found dhcp168:~ giacintogenco$ ~nek5_svn/trunk/nek/makenek -bash: ~nek5_svn/trunk/nek/makenek: No such file or directory dhcp168:~ giacintogenco$ ~/nek5_svn/trunk/nek/makenek makenek - automatic build tool for Nek5000 usage: makenek [.usr filename | clean] < -nocompile > dhcp168:~ giacintogenco$ ~/nek5_svn/trunk/tools/maketools clean make: *** No rule to make target `clean'. Stop. dhcp168:~ giacintogenco$ ~/nek5_svn/trunk/tools/maketools all make: *** No targets specified and no makefile found. Stop. dhcp168:~ giacintogenco$ " What do you suggest me to do ? It seems that I have all the files I need ( X11 , Mac OS X Lion , etc ) but they are "disconnected " . Please if you have a number of instructions I should follow please send me . I will follow all th hints and the instructions you suggest me to do to run the NEK5000 . Thank you ! Best Regards Giacinto Genco

1 5

Question about "taylor" example
by nek5000-users＠lists.mcs.anl.gov 12 Mar '13

12 Mar '13

Hello In the example "taylor", I notice that the radii r0, r1 are set at line no. 191, 192 here http://trac.mcs.anl.gov/projects/nek5/browser/examples/taylor/taylor.usr but then they are modified at line no. 214, 215. I did not understand the reason for this. Changing r0, r1 will change the parameters "a" and "b". Thanks praveen

1 2