January 2016 - Nek5000-users - mailman3.cels.anl.gov

error in generalev
by nek5000-users＠lists.mcs.anl.gov 22 Jan '16

22 Jan '16

Hello Nek, I just met a trouble in running the case ‘high_ray’ In ‘benard’. I changed the original 2X1 calculation field into a 1x1 cavity, and when I ran the case, the error message ‘error in generalev’ appeared on the screen. All elements of the matrix ‘Aeig’ were ‘NaN’. I guess that I made some mistakes in the .usr file, maybe wrong B.C., but I’m not sure. I hope I can get some help from you. Thank you! Kind regards Xu Bolun

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lid driven cavity
by nek5000-users＠lists.mcs.anl.gov 18 Jan '16

18 Jan '16

Hi Neks, I'm trying to solve a simple 2D cavity problem with Nek and I've got the following error: EXIT: E INVALID BC FOUND in genfast 64 * For your info here is the genbox script I used for the mesh: test5.rea 2 spatial dimension 1 number of fields # #======================================================================= # box_1 1st character .ne. "c" or "C" -8 -8 1 nelx,nely,nelz 0 1 1 x_0 x_Nelx ratio 0 1 1 W ,W ,W ,w V bc's ! west,east,south,north,bottom,top * Also, this is the userbc part in user file: c----------------------------------------------------------------------- subroutine userbc (ix,iy,iz,iside,ieg) include 'SIZE' include 'TSTEP' include 'INPUT' include 'NEKUSE' ux=1. uy=0. return end This should be a straightforward problem but am not sure which part I'm getting wrong. Any advice is appreciated. Hopefully, I can make a sample tutorial for this well-known problem and share with new comers. Thanks, Saleh

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Volume average (local)
by nek5000-users＠lists.mcs.anl.gov 18 Jan '16

18 Jan '16

Hi Neks, I am interested in the scalar average inside a specified volume (similar to the glsc2 routine, but only in a small volume). The volume is given by means of the x/y/z-coordinate. V=(x_2-x_1)*(y_2-y_1)*(z_2-z_1), where “1” indicates the lower and “2” the upper coordinate. My first idea was (e.g. for the velocity in streamwise direction): ========================================================= real x1, x2, y1, y2, z1, z2 real lval, lvol, gval, gvol real vxavg integer i,j,k,e [...] ! Specify the volume x1=1.0 x2=2.0 y1=0.0 y2=0.5 z1=0.0 z2=1.0 ! Init lvol=0.0 lval=0.0 gval=0.0 gvol=0.0 ! Loop do e=1,nelt do k=1,nz1 do j=1,ny1 do i=1,nx1 if (xm1(i,j,k,e)>=x1 .and. xm1(i,j,k,e)<=x2 & .and. & ym1(i,j,k,e)>=y1 .and. ym1(i,j,k,e)<=y2 & .and. & zm1(i,j,k,e)>=z1 .and. zm1(i,j,k,e)<=z2 & ) then lvol=lvol+bm1(i,j,k,e) ! Volume lval=lval+vx(i,j,k,e)*bm1(i,j,k,e) ! Weighted scalar value end if end do end do end do end do ! MPI call gop(gval,lval,'+ ',1) call gop(gvol,lvol,'+ ',1) ! Volume averaged streamwise velocity vxavg=gval/gvol ========================================================= This unfortunately doesn't work. Do you see where the problem is? Thanks in advance! Jan F.

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LES equations
by nek5000-users＠lists.mcs.anl.gov 13 Jan '16

13 Jan '16

Hi all, Is the non-linear term in the LES model decomposed in spectral space? Thanks. David

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WARNING: DIV(V)-QTL too large
by nek5000-users＠lists.mcs.anl.gov 12 Jan '16

12 Jan '16

dear developers , I'm doing a rotator-stator type of simulation using Pn-Pn method (lx1=8 lxd=12 ). Annular mesh has been created using genbox (box file is attached). Inner radius is considered as the hub and outer radius is the case (or the sidewalls of the disk ). I use following settings in rea file 3 p27 TORDER 20.00000 p93 Number of prev pressure solns saved 5.000000 p94 start projecting vel. after p94 step 5.000000 p95 start projecting pr after p95 step 4.000000 p99 dealiasing:if <0 disable 1.000000 p101 No. of additional filter modes 5.000000E-02 p103 weight of stabilizing filter (.01) Hub and rotor (z=0) rotating in a constant angular velocity. Stator (z=0.2) and side walls are stationary. singularities among rotor and stationary components are resolved using a method which is very similar to vortex example (using an exponential ramp instead of a polynomial ramp) . After 3000-4000 iterations , CFL number reached around 0.48 and I got following warning L1/L2 DIV(V) : -1.6903E-16 1.0198E-01 L1/L2 QTL : 0.0000E+00 0.0000E+00 L1/L2 DIV(V)-QTL: -1.6903E-16 1.0198E-01 WARNING: DIV(V)-QTL too large! I'm not using any inlets or outlets in my simulation. I'm not sure the reason for this warning. can anybody give me a little advice regarding this situation. I can provide more details on request. Desanga

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VisIt
by nek5000-users＠lists.mcs.anl.gov 11 Jan '16

11 Jan '16

Hi to everyone, this is no an help Nek5000 request. I need the ubuntu 14.04 VisIt installer, can someone send me it? I tried to download it from their web site, but all links seems to be offline. Thanks a lot.

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Re: [Nek5000-users] Nek5000-users Digest, Vol 83, Issue 2
by nek5000-users＠lists.mcs.anl.gov 09 Jan '16

09 Jan '16

Hi Paul, Yes I did do so. The compilation of the case goes fine. After that however, on running nek, instead of generating .dat file, it simply crashes. Note, the case itself runs just fine without the AMG solver, so I know that's not a problem. *Amitvikram Dutta* *MASc Student* *Graduate Research Assistant | Okanagan CFD Laboratory* *Solidification** Processing and Simulation Lab* *School of Engineering* *University of British Columbia | Okanagan Campus* On Sat, Jan 9, 2016 at 10:00 AM, <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. AMG Dump (nek5000-users(a)lists.mcs.anl.gov) > 2. Re: AMG Dump (nek5000-users(a)lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 8 Jan 2016 11:20:23 -0800 > From: nek5000-users(a)lists.mcs.anl.gov > To: nek5000-users(a)lists.mcs.anl.gov > Subject: [Nek5000-users] AMG Dump > Message-ID: > <mailman.13009.1452280844.24727.nek5000-users(a)lists.mcs.anl.gov> > Content-Type: text/plain; charset="utf-8" > > Hi All, > > I'm trying to set up the AMG solver in Nek5000 to solve for the pressures. > I tried following the instructions on Ch5 of the NekDoc available in > github, which contains instructions for running the AMG_Dump. > > However, for some reason I'm unable to generate the *.dat files in my case > folder. I have uncommented the relevant lines in the makenek document and > tried it. However, it doesn't seem to be working. > > Could anyone help out? > > Sincerely, > > *Amitvikram Dutta* > > *MASc Student* > > *Graduate Research Assistant | Okanagan CFD Laboratory* > > *Solidification** Processing and Simulation Lab* > > *School of Engineering* > > *University of British Columbia | Okanagan Campus* >

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AMG Dump
by nek5000-users＠lists.mcs.anl.gov 08 Jan '16

08 Jan '16

Hi All, I'm trying to set up the AMG solver in Nek5000 to solve for the pressures. I tried following the instructions on Ch5 of the NekDoc available in github, which contains instructions for running the AMG_Dump. However, for some reason I'm unable to generate the *.dat files in my case folder. I have uncommented the relevant lines in the makenek document and tried it. However, it doesn't seem to be working. Could anyone help out? Sincerely, *Amitvikram Dutta* *MASc Student* *Graduate Research Assistant | Okanagan CFD Laboratory* *Solidification** Processing and Simulation Lab* *School of Engineering* *University of British Columbia | Okanagan Campus*

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Stress formulation
by nek5000-users＠lists.mcs.anl.gov 05 Jan '16

05 Jan '16

Hi Neks, I have one question about stress formulation in NEK5000. I tried to make a simulation for Poiseuil flow with stress formulation. In inlet boundary condition use was made of parabolic profile. If IFSTRS=false the outlet profile is exactly the same as inlet one but in case of IFSTRS=true the outlet profile changes significantly (both the maximum value and profile shape). Could you tell me how I can get the parabolic profile at outlet, please? The same thing occurs with pressure values. The maximum pressure value with IFSTRS=true is three times higher then the one with IFSTRS=false. I found that the difference comes from subroutines where the stiffness matrix is calculated (axehlm for IFSTRS = false and axhmsf for IFSTRS = true) but I don't undestand what is happening exactly. Thanks in advance for your help, Best regards, Andrew

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