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

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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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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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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Subroutine opdssum
by nek5000-users＠lists.mcs.anl.gov 01 Jun '11

01 Jun '11

Dear all, I was looking into the subroutine "vec_dssum", which is called in "opdssum". At a certain point there is a call to "gs_op_many" (a gather scatter operation I guess, isn't it?) and one of the arguments which is passed to this subroutine is "gsh_fld(ifldt)". I printed to screen the content of "gsh_fld" but I don't understand what is the meaning of it. Thanks in advance for your help. Regards, Andreas.

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Problem with conjugate heat transfer + Low Mach number formulation
by nek5000-users＠lists.mcs.anl.gov 30 May '11

30 May '11

Dear all, I am running a case with conjugate heat transfer + Low Mach number formulation, the domain is a 2D channel. The boundary conditions for the temperature are: - fluid: constant inlet temperature equal to 1; - solid: constant temperature equal to 2 at the outer side, at the inner side there is no boundary condition because the energy equation has to be solved, the other sides are insulated. What I see is that the flow starts to accelerate almost immediately even though at the beginning the temperature of the fluid domain is almost 1. The outlet velocity becomes more than two times the inlet velocity. The reason is that at the wall (and especially at the inlet corner) the thermal divergence is quite large, while it is almost zero in the rest of the fluid domain. In a conjugate heat transfer problem the derivative of the temperature is discontinuos across the wall because of the different thermal conductivities. Could there be a problem when "opgrad" and "opdssum" are evaluated in "subroutine qthermal"? I know that they are evaluated only on the fluid domain but maybe the discontinuity in the derivative of the temperature could give some problems. Thanks a lot in advance for your help. Regards, Andrea

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Subroutine opdssum
by nek5000-users＠lists.mcs.anl.gov 28 May '11

28 May '11

Dear all, I was looking into the subroutine "vec_dssum", which is called in "opdssum". At a certain point there is a call to "gs_op_many" (a gather scatter operation I guess, isn't it?) and one of the arguments which is passed to this subroutine is "gsh_fld(ifldt)". I printed to screen the content of "gsh_fld" but I don't understand what is the meaning of it. Thanks in advance for your help. Regards, Andreas.

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Compilation error
by nek5000-users＠lists.mcs.anl.gov 25 May '11

25 May '11

Hi Nek's, Up to now I have compiled and run the code on the various workstations available in my lab. I am now trying to compile it (only in serial for the moment) on an IBM Power 6 ( http://www.idris.fr/su/Scalaire/vargas/hw-vargas.html) but I encounter an error (which is the reason why I do not compile it using mpi support yet). Following is the outpost from the compilation: xlf_r -qsuppress=cmpmsg -o nek5000 obj/stenosis.o obj/drive.o obj/drive1.o obj/drive2.o obj/plan4.o obj/bdry.o obj/coef.o obj/conduct.o obj/connect1.o obj/connect2.o obj/dssum.o obj/edgec.o obj/eigsolv.o obj/gauss.o obj/genxyz.o obj/navier1.o obj/makeq.o obj/navier0.o obj/navier2.o obj/navier3.o obj/navier4.o obj/prepost.o obj/speclib.o obj/map2.o obj/turb.o obj/mvmesh.o obj/ic.o obj/ssolv.o obj/planx.o obj/math.o obj/mxm_wrapper.o obj/hmholtz.o obj/gfdm_par.o obj/gfdm_op.o obj/gfdm_solve.o obj/subs1.o obj/subs2.o obj/genbox.o obj/gmres.o obj/hsmg.o obj/convect.o obj/induct.o obj/perturb.o obj/navier5.o obj/navier6.o obj/navier7.o obj/navier8.o obj/fast3d.o obj/fasts.o obj/calcz.o obj/byte.o obj/chelpers.o obj/byte_mpi.o obj/postpro.o obj/cvode_driver.o obj/nek_comm.o obj/init_plugin.o obj/setprop.o obj/qthermal.o obj/cvode_aux.o obj/makeq_aux.o obj/papi.o obj/ssygv.o obj/dsygv.o obj/mxm_std.o obj/blas.o obj/comm_mpi.o obj/mpi_dummy.o obj/singlmesh.o obj/jl2_gs.o obj/jl2_sort.o obj/jl2_sarray_transfer.o obj/jl2_sarray_sort.o obj/jl2_gs_local.o obj/jl2_crystal.o obj/jl2_comm.o obj/jl2_tensor.o obj/jl2_fail.o obj/jl2_fcrystal.o obj/jl_tuple_list.o obj/jl_transfer.o obj/jl_sort.o obj/jl_fcrystal.o obj/jl_errmem.o obj/jl_crystal.o obj/jl2_findpts.o obj/jl2_findpts_local.o obj/jl2_obbox.o obj/jl2_poly.o obj/jl2_lob_bnd.o obj/jl2_findpts_el_3.o obj/jl2_findpts_el_2.o obj/jl2_sparse_cholesky.o obj/jl2_xxt.o obj/jl2_fcrs.o ld: 0711-317 ERROR: Undefined symbol: .etime ld: 0711-345 Use the -bloadmap or -bnoquiet option to obtain more information. gmake: *** [nek5000] Error 8 Attached is the whole compiler.out file also. Does anyone have an idea? Regards, -- Jean-Christophe

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Average in arbitrary direction
by nek5000-users＠lists.mcs.anl.gov 22 May '11

22 May '11

Hello Neks, I have looked at the turbChannel example for an example on planar averaging. However, I was wondering if there was any advice on how to do this if the elements aren't exactly "nice"... (i.e., the elements may have arbitrary rotations) Specifically, I have a pipe flow, and I am wanting to do an average in the z (axial) direction. My initial thoughts were to interpolate my values to set R, theta components, and then average this along z. I'm stuck on the best way to do either one of these operations, however (especially because I would like to use an integration rule to compute the average in the z direction). If anyone could point me in the right direction, that would be a big help. Thanks! -- Josh Camp "All that is necessary for the triumph of evil is that good men do nothing" -- Edmund Burke

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