December 2012 - 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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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

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Visit reader for double precision f files
by nek5000-users＠lists.mcs.anl.gov 06 Mar '13

06 Mar '13

//Dear Neks, // Reference to previous discussion (Sep.13th) about the support for the reading 64 bit files of nek5000 in VisIt, we have put up together a 3D cylinder as test case. For a double-precision format nek5000 dump file the 3D view and especially iso-contours are working fine whereas any 2D projection slice, or cut of the data is not working properly. In general operations considering the whole grid seem to work fine, but those related to a section of the grid such as box don't. This anomaly is happening regardless of choosing various pressure solver scheme (Pn_Pn/Pn_Pn-2) or including the grid data to be dumped in the file or not. I was wondering if you can help me with this issue. With many thanks Reza P.S. The 3D cylinder test-case located at the origin (0,0,0) of the coordinate system and extruded along the z-axis (perpendicular to the xy plane). The box extends from -15 to 25 in x direction, -9 to 9 in y direction and -2 to 2 in z directions. The mesh is constructed from the 2D cylinder in nek5000 repository. The number of elements is reduced, then extended in the z direction. An example of the dumped file can be found in the ftn: ftp://ftp.mech.kth.se/pub/pschlatt/nek5000

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opdiv and multd
by nek5000-users＠lists.mcs.anl.gov 10 Feb '13

10 Feb '13

Hi all, I am having some problems using the subroutines opdiv and multd. For some reasons they do not give me correct results. Do they need any special treatment or precautions? I was trying to compute the divergence of a 3D field, and i realized that in my case the multd subroutine used by opdiv does not gives good results, while the same derivative computed from gram1 gives no problems. For example, I overwrite an analytical field : ... parameter(lt=lx1*ly1*lz1*lelt) real Res(lt) ... vx(i,j,k,e)= 1.0*sin(x)*cos(y)*cos(z) ... call print_line(vx) ... iflg = 1 call multd (RES(1),vx,rym2,sym2,tym2,2,iflg) call print_line(Res(1) ) call gradm1(work1,Res(1),work2,vx) call print_line(Res(1) ) ... if (lx2.ne.lx1) then ... STOP endif and print output a (xr,:,zr) the result (performed by print_line) . In vxi.eps i compare the result (lines) with the analytical solution( symbols). The result of multd is not correct while all the others match perfectly the analytical solution. In vxy.eps i plot only the result of multd. Note that on y i have 12 elements the same number of peaks of the solution. Does anybody have an idea on how to fix this? Thank you very much for any help or suggestion francesco

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mesh problems
by nek5000-users＠lists.mcs.anl.gov 14 Jan '13

14 Jan '13

Dear Neks, I generated a big mesh with 7948800 elements for a cylindrical cell of aspect ratio 3, i.e. x between -1.5 and 1.5 y between -1.5 and 1.5 z between 0 and 1 prex, n2to3, reatore2, amgdump and genmap worked. The AMG preconditioning with go.m worked as well (runtime 3.5 weeks). prex started out of 3 basic elements which were refined with multi split into Element1: 90, 90 subelements Element2: 70, 90 Element3: 70, 90 stretch, r, factor 3 I started the job on BG/Q and get the following error messages in the output file: bash-4.1$ m G3_96.out.0 /----------------------------------------------------------\ | _ __ ______ __ __ ______ ____ ____ ____ | | / | / // ____// //_/ / ____/ / __ \ / __ \ / __ \ | | / |/ // __/ / ,< /___ \ / / / // / / // / / / | | / /| // /___ / /| | ____/ / / /_/ // /_/ // /_/ / | | /_/ |_//_____//_/ |_|/_____/ \____/ \____/ \____/ | | | |----------------------------------------------------------| | | | NEK5000: Open Source Spectral Element Solver | | COPYRIGHT (c) 2008-2010 UCHICAGO ARGONNE, LLC | | Version: 1.0rc1 / SVN r838 | | Web: http://nek5000.mcs.anl.gov | | | \----------------------------------------------------------/ Number of processors: 65536 REAL wdsize : 8 INTEGER wdsize : 4 Beginning session: /homec/hil02/hil020/nek5_svn/g396_r097_Lx1_08_Ra1e9/G3_96.rea timer accuracy: 1.4962500E-07 sec read .rea file read .re2 file byte swap: T -0.2931277218E+36 6.543210030 nelgt/nelgv/lelt: 7948800 7948800 150 lx1 /lx2 /lx3 : 4 2 4 mapping elements to processors element load imbalance: 1 121 122 done :: mapping elements to processors reading mesh reading curved sides reading bc for ifld 1 reading bc for ifld 2 done :: read .re2 file 0 objects found done :: read .rea file 496.34 sec Reset the target Courant number to .5 setup mesh topology Right-handed check complete for 7948800 elements. OK. setvert3d: 4 152084809 215675209 152084809 152084809 call usrsetvert done :: usrsetvert gs_setup: 50336837 unique labels shared pairwise times (avg, min, max): 0.00330717 0.000218656 0.00853093 crystal router : 0.0077495 0.00761262 0.00818637 used all_to_all method: crystal router setupds time 6.1645E-01 seconds 0 4 152084809 7948800 8 max multiplicity done :: setup mesh topology call usrdat done :: usrdat generate geomerty data vol_t,vol_v: 7.06857958483581861 7.06857958483581861 done :: generate geomerty data call usrdat2 done :: usrdat2 regenerate geomerty data 1 vol_t,vol_v: 7.06857958483581861 7.06857958483581861 done :: regenerate geomerty data 1 verify mesh topology -1.50001142304138035 1.50001142290878886 Xrange -1.50001142298026835 1.50001142292693612 Yrange 0.000000000000000000E+00 1.00000000000000000 Zrange WARNING1 Element mesh mismatch at: WARNING1 Element mesh mismatch at: WARNING1 Element mesh mismatch at: WARNING1 Element mesh mismatch at: WARNING1 Element mesh mismatch at: WARNING1 Element mesh mismatch at: WARNING1 Element mesh mismatch at: WARNING1 Element mesh mismatch at: WARNING1 Element mesh mismatch at: WARNING1 Element mesh mismatch at: WARNING1 Element mesh mismatch at: WARNING1 Element mesh mismatch at: WARNING1 Element mesh mismatch at: WARNING1 Element mesh mismatch at: WARNING1 Element mesh mismatch at: i,j,k,ie: 4 2 1 954634 i,j,k,ie: 1 2 1 916744 i,j,k,ie: 2 4 2 972970 i,j,k,ie: 2 1 1 931570 WARNING1 Element mesh mismatch at: i,j,k,ie: 4 2 1 957874 WARNING1 Element mesh mismatch at: i,j,k,ie: 4 2 1 996664 Near X = -.12308168E-01 -.34092836 .60036000E-01, d: .12947845E-04 .00000000E+00 81.225474 WARNING1 Element mesh mismatch at: Near X = .11336871E-01 -.82826699 .61838637E-01, d: .00000000E+00 -.11766071E-04 88.069931 Near X = .97128875E-05 .82845591 .60036000E-01, d: .00000000E+00 -.20015559E-04 88.069931 i,j,k,ie: 2 1 1 981007 WARNING1 Element mesh mismatch at: i,j,k,ie: 2 1 1 939607 i,j,k,ie: 4 2 4 995854 WARNING1 Element mesh mismatch at: WARNING1 Element mesh mismatch at: WARNING1 Element mesh mismatch at: WARNING1 Element mesh mismatch at: i,j,k,ie: 2 4 3 972989 WARNING1 Element mesh mismatch at: i,j,k,ie: 2 4 4 931590 Near X = .12193251E-01 .42841310 .66558003E-01, d: .00000000E+00 -.12947474E-04 81.991313 WARNING1 Element mesh mismatch at: i,j,k,ie: 4 2 4 916204 WARNING1 Element mesh mismatch at: WARNING1 Element mesh mismatch at: WARNING1 Element mesh mismatch at: i,j,k,ie: 1 2 4 958144 WARNING1 Element mesh mismatch at: WARNING1 Element mesh mismatch at: WARNING1 Element mesh mismatch at: WARNING1 Element mesh mismatch at: WARNING1 Element mesh mismatch at: WARNING1 Element mesh mismatch at: WARNING1 Element mesh mismatch at: WARNING1 Element mesh mismatch at: WARNING1 Element mesh mismatch at: Near X = .12320624E-01 .31593135 .73282003E-01, d: .12573222E-04 .00000000E+00 81.079569 i,j,k,ie: 3 2 4 541894 WARNING1 Element mesh mismatch at: WARNING1 Element mesh mismatch at: WARNING1 Element mesh mismatch at: i,j,k,ie: 2 1 1 981003 WARNING1 Element mesh mismatch at: i,j,k,ie: 2 4 1 939603 WARNING1 Element mesh mismatch at: WARNING1 Element mesh mismatch at: WARNING1 Element mesh mismatch at: i,j,k,ie: 2 4 4 890151 WARNING1 Element mesh mismatch at: Near X = -.62894639E-05 -1.1769232 .60036000E-01, d: .15284684E-04 .00000000E+00 92.459135 WARNING1 Element mesh mismatch at: Near X = .63923475E-05 1.1769232 .60036000E-01, d: .00000000E+00 -.15284684E-04 92.458255 i,j,k,ie: 3 2 4 2524 i,j,k,ie: 3 2 4 624964 Near X = -.10302672E-04 .82845591 .60036000E-01, d: .20015559E-04 .00000000E+00 88.062609 i,j,k,ie: 2 4 4 62171 i,j,k,ie: 2 4 4 600363 WARNING1 Element mesh mismatch at: WARNING1 Element mesh mismatch at: WARNING1 Element mesh mismatch at: --------------------------------------------------------- and so on……. The job hangs at this position and does not continue. Can it be that the precision of the coordinate ranges is not sufficient? For a job that runs well (here an aspect ratio one cell as an example) I got in the output file the following coordinates. …… verify mesh topology -0.500000000000000000 0.500000000000000000 Xrange -0.500000000000000000 0.500000000000000000 Yrange 0.000000000000000000E+00 1.00000000000000000 Zrange done :: verify mesh topology …… i.e. precise bounds down to the last digit. Note also that I had to adapt the programs n2to3 and reatore2, e.g.: [josc1234@reynolds n2to3]$ diff n2to3.f n2to3.f_orig 31c31 < parameter(nelm=99999) --- > parameter(nelm=9999) [josc1234@reynolds reatore2]$ diff reatore2.f reatore2.f_orig 19c19 < parameter(lelt=10000000) --- > parameter(lelt=1000000) 118c118 I wonder if you have an idea where things went wrong? Is it already the prex? Thanks for your help in advance. Best regards, Joerg.

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