June 2011 - Nek5000-users - mailman3.cels.anl.gov

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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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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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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Periodic B.C and Genmap Issue
by nek5000-users＠lists.mcs.anl.gov 09 Nov '12

09 Nov '12

Hi Paul, This post is in reference to the previous post by Michael (dated Jun 22). When I try to get a map file for a rea file that has periodic vertices, I get the following error. The rea file was generated the same way as before (Gambit -> Nek through Matlab). I checked on Matlab by plotting the periodic vertices and confirmed for a few faces that they are indeed periodic. Also, as you had earlier suggested (with the new genmap), I tried changing the tolerances fro 0.09 to 0.2 and I get the same periodic mismatch error. Could you provide any leads on where things are going wrong ? Please find below the error message. Thanks. <error> Input (.rea) file name: domain Input mesh tolerance (default 0.2): NOTE: smaller is better, but generous is more forgiving for bad meshes. 0.09 reading .rea file data ... start locglob_lexico: 8 3912 31296 8.99999999999999967E-002 locglob: 1 1 31296 locglob: 2 36 31296 locglob: 3 1224 31296 locglob: 1 4851 31296 locglob: 2 4851 31296 locglob: 3 4851 31296 locglob: 1 4851 31296 locglob: 2 4851 31296 locglob: 3 4851 31296 done locglob_lexico: 4851 4851 31296 10 start periodic vtx: 3912 4851 abort: PERIODIC MISMATCH 2: 1093 1 P ie 0 1 je 4.14470000000000029E-003 0.0000000000000000 bc 8 quit </error> Regards Shriram

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Lagrangian Particle Tracking
by nek5000-users＠lists.mcs.anl.gov 22 Mar '12

22 Mar '12

Hi, I have couple of questions regarding the subroutine given for Lagrangian particle tracking at the following wiki page and I wonder if there are any hints. http://nek5000.mcs.anl.gov/index.php/Data_processing_example - Where should this subroutine be inserted? - What are the variables "rtl" and "mr" representing? - How to set the initial positions of the particles? - Should the constant parameters "npart" and "dt_p" be inserted in SIZE file? Thanks in advance, Regards, Alireza Karimi

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Re: [Nek5000-users] Running Simulations in Parallel with nekbmpi
by nek5000-users＠lists.mcs.anl.gov 27 Sep '11

27 Sep '11

Hi, I have lp=512 in SIZE, and I did compile with IFMPI=true. I recompiled yesterday because I thought this may be the case, but I was still getting the same error. When I first start a simulation and run top, it shows four processors running nek5000, but this changes to one processor after a few seconds. Thanks, John

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Re : CYCLIC BC for bend pipe
by nek5000-users＠lists.mcs.anl.gov 29 Jun '11

29 Jun '11

On Mon, 2011-06-27 at 12:00 -0500, nek5000-users-request(a)lists.mcs.anl.gov wrote: > Re : CYCLIC BC for bend pipe Dear Paul; This is exactly what I wanted. I tested the example and it works very well. Many thanks for the useful information. Best regards; Azad

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Re : CYCLIC BC for bend pipe
by nek5000-users＠lists.mcs.anl.gov 26 Jun '11

26 Jun '11

Hi Paul; Since I am using Prenek to generate the base mesh for the pipe in X-Y plane, and then extrude it in the Z direction using the n2to3 tool, is there any easy way to change the orientation of such a mesh based on your suggestion? Or maybe I need to start generating the grid from the very beginning in X-Z plane? Best regards Azad PS - be sure that the rotation preserves the right-handed coordinates of the original system. On Sun, 26 Jun 2011, nek5000-users at lists.mcs.anl.gov wrote: > > Hi Azad, > > It's important that the "cyclic" axis be the z-axis. > > You may need to rotate your geometry into this orientation. > > In that case, your inlet/out planes would, say, be x-z > and y-z planes. > > Paul > > > On Sun, 26 Jun 2011, nek5000-users at lists.mcs.anl.gov wrote: > >> Dear Neks; >> >> I had a question regarding cyclic bc. It works properly for 2D and 3D >> curved channel, (arch-like curvature is generated in stream-wise >> direction using userdat2 with period bc at the both ends). However, when >> I try it for the curved pipe, seems not working at all. I appreciate it >> if you could help me by that. >> >> Many thanks; >> Azad >> >>

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CYCLIC BC for bend pipe
by nek5000-users＠lists.mcs.anl.gov 26 Jun '11

26 Jun '11

Dear Neks; I had a question regarding cyclic bc. It works properly for 2D and 3D curved channel, (arch-like curvature is generated in stream-wise direction using userdat2 with period bc at the both ends). However, when I try it for the curved pipe, seems not working at all. I appreciate it if you could help me by that. Many thanks; Azad

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Adjoint perturbation
by nek5000-users＠lists.mcs.anl.gov 21 Jun '11

21 Jun '11

Hi Nek's, I am interested into the linear adjoint perturbation. The equations read: -du/dt = (U.Grad) u - transpose(Grad(U)) u + 1/Re Laplacian(u) - grad(p) div(u) = 0 Assuming t' = T-t, one can rewrite: du/dt' = (U.Grad) u - transpose(Grad(U)) u + 1/Re Laplacian(u) - grad(p) Only small modifications to the perturbation mode are necessary, mainly to evaluate the tranpose gradient terms. Here is what I've done to evaluate these: subroutine conv_adj(conv_x,conv_y,conv_z,u_x,u_y,u_z) ! used to be conv1n include 'SIZE' include 'DXYZ' include 'INPUT' include 'GEOM' include 'SOLN' include 'TSTEP' parameter (lt=lx1*ly1*lz1*lelt) real u_x (size(vx,1),size(vx,2),size(vx,3),size(vx,4)) real u_y (size(vx,1),size(vx,2),size(vx,3),size(vx,4)) real u_z (size(vx,1),size(vx,2),size(vx,3),size(vx,4)) real u_xx (size(vx,1),size(vx,2),size(vx,3),size(vx,4)) real u_xy (size(vx,1),size(vx,2),size(vx,3),size(vx,4)) real u_xz (size(vx,1),size(vx,2),size(vx,3),size(vx,4)) real u_yx (size(vy,1),size(vy,2),size(vy,3),size(vy,4)) real u_yy (size(vy,1),size(vy,2),size(vy,3),size(vy,4)) real u_yz (size(vy,1),size(vy,2),size(vy,3),size(vy,4)) real u_zx (size(vz,1),size(vz,2),size(vz,3),size(vz,4)) real u_zy (size(vz,1),size(vz,2),size(vz,3),size(vz,4)) real u_zz (size(vz,1),size(vz,2),size(vz,3),size(vz,4)) real conv_x (size(vx,1),size(vx,2),size(vx,3),size(vx,4)) real conv_y (size(vy,1),size(vy,2),size(vy,3),size(vy,4)) real conv_z (size(vz,1),size(vz,2),size(vz,3),size(vz,4)) *call gradm1(u_xx,u_xy,u_xz,u_x)* * call gradm1(u_yx,u_yy,u_yz,u_y)* * call gradm1(u_zx,u_zy,u_zz,u_z)* * * * conv_x = vx*u_xx + vy*u_yx + vz*u_zx* * conv_y = vx*u_xy + vy*u_yy + vz*u_zy* * conv_z = vx*u_xz + vy*u_yz + vz*u_zz* return end However, I'm not sure I've done it properly or not (arrays declaration for instance). Especially, I had no idea wheter I have to use the gradm1 subroutine or its weak counterpart wgradm1. Finally in perturb.f, I've slightly change the advap subroutine the following way: subroutine advabp C C Eulerian scheme, add convection term to forcing function C at current time step. C include 'SIZE' include 'INPUT' include 'SOLN' include 'MASS' include 'TSTEP' C COMMON /SCRNS/ TA1 (LX1*LY1*LZ1*LELV) $ , TA2 (LX1*LY1*LZ1*LELV) $ , TA3 (LX1*LY1*LZ1*LELV) $ , TB1 (LX1*LY1*LZ1*LELV) $ , TB2 (LX1*LY1*LZ1*LELV) $ , TB3 (LX1*LY1*LZ1*LELV) C ntot1 = nx1*ny1*nz1*nelv ntot2 = nx2*ny2*nz2*nelv c if (if3d) then call opcopy (tb1,tb2,tb3,vx,vy,vz) ! Save velocity call opcopy (vx,vy,vz,vxp(1,jp),vyp(1,jp),vzp(1,jp)) ! U <-- du * call conv_adj(ta1,ta2,ta3,tb1,tb2,tb3)* * call opcopy (vx,vy,vz,tb1,tb2,tb3) ! Restore velocity* *c* * do i=1,ntot1* * tmp = bm1(i,1,1,1)*vtrans(i,1,1,1,ifield)* * bfxp(i,jp) = bfxp(i,jp)-tmp*ta1(i)* * bfyp(i,jp) = bfyp(i,jp)-tmp*ta2(i)* * bfzp(i,jp) = bfzp(i,jp)-tmp*ta3(i)* * enddo* c call convop (ta1,vxp(1,jp)) ! U.grad dU call convop (ta2,vyp(1,jp)) call convop (ta3,vzp(1,jp)) c do i=1,ntot1 tmp = bm1(i,1,1,1)*vtrans(i,1,1,1,ifield) *bfxp(i,jp) = bfxp(i,jp) + tmp*ta1(i)* * bfyp(i,jp) = bfyp(i,jp) + tmp*ta2(i)* * bfzp(i,jp) = bfzp(i,jp) + tmp*ta3(i)* enddo c else ! 2D c call opcopy (tb1,tb2,tb3,vx,vy,vz) ! Save velocity call opcopy (vx,vy,vz,vxp(1,jp),vyp(1,jp),vzp(1,jp)) ! U <-- dU call convop (ta1,tb1) ! du.grad U call convop (ta2,tb2) call opcopy (vx,vy,vz,tb1,tb2,tb3) ! Restore velocity c do i=1,ntot1 tmp = bm1(i,1,1,1)*vtrans(i,1,1,1,ifield) bfxp(i,jp) = bfxp(i,jp)-tmp*ta1(i) bfyp(i,jp) = bfyp(i,jp)-tmp*ta2(i) enddo c call convop (ta1,vxp(1,jp)) ! U.grad dU call convop (ta2,vyp(1,jp)) c do i=1,ntot1 tmp = bm1(i,1,1,1)*vtrans(i,1,1,1,ifield) bfxp(i,jp) = bfxp(i,jp)-tmp*ta1(i) bfyp(i,jp) = bfyp(i,jp)-tmp*ta2(i) enddo c endif c return end Any help to spot potential erros or to speed up these operation would be highly appreciated. Best regards, -- Jean-Christophe

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