January 2018 - Nek5000-users - mailman3.cels.anl.gov

Re: [Nek5000-users] Re post-processing using f0000 files
by nek5000-users＠lists.mcs.anl.gov 12 Jan '18

12 Jan '18

Hi Ketan, Yes there are 288 elements indeed. As far as I can see it outpost the rms and TKE in the code. May I know where it output the mean velocity? lt = lx1*ly1*lz1*nelt ifld = 1 ccc avg all the avgp10.f0* files call auto_averager(fname1) ccc copy uk=vx**2, vk=vy**2, wk=vz**2 call col3(uk,vx,vx,lt) call col3(vk,vy,vy,lt) call col3(wk,vz,vz,lt) ccc avg all the rmsp10.f0* files call auto_averager(fname2) ccc u'^2,v'^2,w'^2 = rms - avg**2 call sub2(vx,uk,lt) call sub2(vy,vk,lt) call sub2(vz,wk,lt) ccc Average in the z direction call my_z_avg(uk,vx,gs_avg_hndl,nelxy,ifld) call my_z_avg(vk,vy,gs_avg_hndl,nelxy,ifld) call my_z_avg(wk,vz,gs_avg_hndl,nelxy,ifld) ccc TKE = 0.5*(u'^2+v'^2+w'^2) call add4(pk,uk,vk,wk,lt) call cmult(pk,0.5,lt) ccc sqrt uk,vk,wk to get urms, vrms and wrms call vsqrt(uk,lt) call vsqrt(vk,lt) call vsqrt(wk,lt) ccc output urms**2,vrms**2 and wrms**2 along with the TKE ccc TKE is in pressure field call outpost(uk,vk,wk,pk,t,' ') Kind regards, ZJ

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ERROR: e-solver does not exist
by nek5000-users＠lists.mcs.anl.gov 12 Jan '18

12 Jan '18

Im trying to make a turbulance flow 2d rectangular box and getting this error /----------------------------------------------------------\\ | _ __ ______ __ __ ______ ____ ____ ____ | | / | / // ____// //_/ / ____/ / __ \\/ __ \\/ __ \\ | | / |/ // __/ / ,< /___ \\ / / / // / / // / / / | | / /| // /___ / /| | ____/ / / /_/ // /_/ // /_/ / | | /_/ |_//_____//_/ |_|/_____/ \\___/ \\___/ \\___/ | | | |----------------------------------------------------------| | | | NEK5000: Open Source Spectral Element Solver | | COPYRIGHT (c) 2008-2017 UCHICAGO ARGONNE, LLC | | Version: v17.0 | | Web: http://nek5000.mcs.anl.gov | | | \\----------------------------------------------------------/ Number of processors: 8 REAL wdsize : 8 INTEGER wdsize : 4 Timer accuracy : 4.83E-08 Reading /home/Nek5000/run/git/NewBarc/NewBarc.rea Reading /home/Nek5000/run/git/NewBarc/NewBarc.re2 mapping elements to processors Reading /home/Nek5000/run/git/NewBarc/NewBarc.ma2 0 91 91 730 730 NELV 1 91 91 730 730 NELV 2 91 91 730 730 NELV 3 92 92 730 730 NELV 4 91 91 730 730 NELV 5 91 91 730 730 NELV 6 91 91 730 730 NELV 7 92 92 730 730 NELV RANK 0 IEG 351 352 353 354 355 356 381 382 383 384 385 386 387 388 389 391 392 393 394 395 396 397 398 399 401 402 403 404 405 406 407 408 409 411 412 413 414 415 416 417 418 419 421 422 423 424 425 426 427 428 429 431 432 433 434 435 436 437 438 441 442 443 444 445 446 447 448 451 452 453 454 455 456 457 458 461 462 463 464 465 466 467 468 471 472 473 474 475 476 477 478 element load imbalance: 1 91 92 done :: mapping 0.13924E-02 sec preading mesh preading bc for ifld 1 done :: read .re2 file 0.45E-02 sec 0 objects found 103 Parameters from file: 1 1.000000 p01 DENSITY 2 -40000.00 p02 VISCOS 11 280000.000 p11 NSTEPS 12 -.10000000E-04 p12 DT 15 500.0000 p15 IOSTEP 21 1.0000000E-05 22 1.0000000E-08 p22 HELMHOLTZ 24 1.0000000E-02 p24 TOLREL 25 1.0000000E-02 p25 TOLABS 26 2.000000 p26 COURANT/NTAU 27 3.000000 p27 TORDER 59 0.0000000E+00 p59 !=0 --> use std axhelm for all elem 65 1.0000000E+00 p65 #iofile(eg,0 or 64); <0 --> sep. dirs 66 6.000000 p66 write fmt:ONLY postx uses rea value 67 6.000000 p67 read fmt: same modes as p66 68 200000.00E+00 p68 iastep: freq for avg_all 93 20.00000 p93 Numbr of prev pressure solns saved 94 5.000000 p94 start projecting vel. after p94 step 95 5.000000 p95 start projecting pr after p95 step 99 4.000000 p99 dealiasing:if <0 disable 101 2.0000000E+00 p101 No. of additional filter modes 103 5.0000000E-01 p103 weight of stabilizing filter (.01) done :: read .rea file 0.85864E-02 sec nelgt/nelgv/lelt: 730 730 92 lx1 /lx2 /lx3 : 6 6 6 setup mesh topology Right-handed check complete for 730 elements. OK. setvert2d: 6 6880 18560 6880 6880 call usrsetvert done :: usrsetvert gs_setup: 507 unique labels shared pairwise times (avg, min, max): 4.50263e-06 4.3549e-06 4.572e-06 crystal router : 7.19253e-06 7.1082e-06 7.2708e-06 all reduce : 9.94137e-05 9.93523e-05 9.9448e-05 used all_to_all method: pairwise handle bytes (avg, min, max): 22683 22012 23620 buffer bytes (avg, min, max): 2084 1648 2720 setupds time 1.0156E-02 seconds 0 6 6880 730 4 max multiplicity done :: setup mesh topology call usrdat done :: usrdat generate geometry data NOTE: All elements deformed , param(59) ^=0 done :: generate geometry data call usrdat2 done :: usrdat2 regenerate geometry data 1 NOTE: All elements deformed , param(59) ^=0 done :: regenerate geometry data 1 verify mesh topology -2.3561944901923448 3.9269908169872418 Xrange -1.0000000000000000 1.0000000000000000 Yrange 9.9000000000000010E+021 -9.9000000000000010E+021 Zrange done :: verify mesh topology IFTRAN = T IFFLOW = T IFHEAT = F IFSPLIT = T IFLOMACH = F IFUSERVP = F IFUSERMV = F IFPERT = F IFADJ = F IFSTRS = F IFCHAR = T IFCYCLIC = F IFAXIS = F IFMVBD = F IFMELT = F IFNEKNEK = F IFSYNC = F IFVCOR = F IFINTQ = F IFGEOM = F IFSURT = F IFWCNO = F IFTMSH for field 1 = F IFADVC for field 1 = T IFNONL for field 1 = F Dealiasing enabled, lxd= 9 Estimated eigenvalues EIGAA = 1.3587005501361697 EIGGA = 1269143.4772368053 EIGAE = 0.25000000000000000 EIGAS = 2.2999917087593809E-002 EIGGE = 1269143.4772368053 EIGGS = 2.0000000000000000 verify mesh topology -2.3561944901923448 3.9269908169872418 Xrange -1.0000000000000000 1.0000000000000000 Yrange 9.9000000000000010E+021 -9.9000000000000010E+021 Zrange done :: verify mesh topology E-solver strategy: 0 itr mg_nx: 1 3 5 mg_ny: 1 3 5 mg_nz: 0 0 0 call usrsetvert done :: usrsetvert gs_setup: 103 unique labels shared pairwise times (avg, min, max): 2.35579e-06 2.2701e-06 2.4383e-06 crystal router : 4.06828e-06 3.9056e-06 4.3852e-06 all reduce : 4.63608e-06 4.5825e-06 4.698e-06 used all_to_all method: pairwise handle bytes (avg, min, max): 4695 4540 4900 buffer bytes (avg, min, max): 468 368 608 setupds time 9.6015E-04 seconds 1 2 792 730 setvert2d: 4 3836 6756 3836 3836 call usrsetvert done :: usrsetvert gs_setup: 305 unique labels shared pairwise times (avg, min, max): 2.88736e-06 2.7693e-06 2.9417e-06 crystal router : 5.67697e-06 5.5738e-06 5.7281e-06 all reduce : 1.5845e-05 7.419e-06 2.43007e-05 used all_to_all method: pairwise handle bytes (avg, min, max): 13689 13276 14260 buffer bytes (avg, min, max): 1276 1008 1664 setupds time 2.7936E-03 seconds 2 4 3836 730 setvert2d: 4 3836 6756 3836 3836 call usrsetvert done :: usrsetvert gs_setup: 305 unique labels shared pairwise times (avg, min, max): 2.74806e-06 2.6386e-06 2.849e-06 crystal router : 5.45844e-06 5.3276e-06 5.5491e-06 all reduce : 7.42733e-06 7.3395e-06 7.5135e-06 used all_to_all method: pairwise handle bytes (avg, min, max): 13689 13276 14260 buffer bytes (avg, min, max): 1276 1008 1664 setupds time 1.7463E-03 seconds 3 4 3836 730 setvert2d: 6 6880 18560 6880 6880 call usrsetvert done :: usrsetvert gs_setup: 507 unique labels shared pairwise times (avg, min, max): 2.98656e-06 2.8975e-06 3.0673e-06 crystal router : 1.37999e-05 1.36954e-05 1.38856e-05 all reduce : 1.64007e-05 1.62838e-05 1.65981e-05 used all_to_all method: pairwise handle bytes (avg, min, max): 22683 22012 23620 buffer bytes (avg, min, max): 2084 1648 2720 setupds time 2.4769E-03 seconds 4 6 6880 730 regenerate geometry data 1 NOTE: All elements deformed , param(59) ^=0 done :: regenerate geometry data 1 h1_mg_nx: 1 3 5 h1_mg_ny: 1 3 5 h1_mg_nz: 0 0 0 call usrsetvert done :: usrsetvert gs_setup: 103 unique labels shared pairwise times (avg, min, max): 2.37065e-06 2.3153e-06 2.4607e-06 crystal router : 3.88401e-06 3.7749e-06 3.9709e-06 all reduce : 4.90976e-06 4.8233e-06 5.0116e-06 used all_to_all method: pairwise handle bytes (avg, min, max): 4695 4540 4900 buffer bytes (avg, min, max): 468 368 608 setupds time 9.4292E-04 seconds 5 2 792 730 setvert2d: 4 3836 6756 3836 3836 call usrsetvert done :: usrsetvert gs_setup: 305 unique labels shared pairwise times (avg, min, max): 2.91439e-06 2.7588e-06 3.0219e-06 crystal router : 5.61719e-06 5.5624e-06 5.6535e-06 all reduce : 7.48192e-06 7.4368e-06 7.5201e-06 used all_to_all method: pairwise handle bytes (avg, min, max): 13689 13276 14260 buffer bytes (avg, min, max): 1276 1008 1664 setupds time 2.3787E-03 seconds 6 4 3836 730 setvert2d: 4 3836 6756 3836 3836 call usrsetvert done :: usrsetvert gs_setup: 305 unique labels shared pairwise times (avg, min, max): 2.94944e-06 2.7296e-06 3.1507e-06 crystal router : 5.54658e-06 5.4843e-06 5.5919e-06 all reduce : 7.52008e-06 7.3959e-06 7.6057e-06 used all_to_all method: pairwise handle bytes (avg, min, max): 13689 13276 14260 buffer bytes (avg, min, max): 1276 1008 1664 setupds time 1.8404E-03 seconds 7 4 3836 730 setvert2d: 6 6880 18560 6880 6880 call usrsetvert done :: usrsetvert gs_setup: 507 unique labels shared pairwise times (avg, min, max): 3.04339e-06 2.9536e-06 3.1081e-06 crystal router : 7.14937e-06 7.0897e-06 7.1979e-06 all reduce : 1.48502e-05 1.47878e-05 1.49567e-05 used all_to_all method: pairwise handle bytes (avg, min, max): 22683 22012 23620 buffer bytes (avg, min, max): 2084 1648 2720 setupds time 2.3173E-03 seconds 8 6 6880 730 setvert2d: 6 6880 18560 6880 6880 call usrsetvert done :: usrsetvert gs_setup: 507 unique labels shared pairwise times (avg, min, max): 2.87688e-06 2.7267e-06 2.9336e-06 crystal router : 7.30052e-06 7.2595e-06 7.3437e-06 all reduce : 1.4766e-05 1.46617e-05 1.48032e-05 used all_to_all method: pairwise handle bytes (avg, min, max): 22683 22012 23620 buffer bytes (avg, min, max): 2084 1648 2720 setupds time 2.2158E-03 seconds 9 6 6880 730 setvert2d: 8 9924 36204 9924 9924 call usrsetvert done :: usrsetvert gs_setup: 709 unique labels shared pairwise times (avg, min, max): 3.12636e-06 2.9746e-06 3.2381e-06 crystal router : 8.53711e-06 8.4963e-06 8.5871e-06 all reduce : 1.69634e-05 1.68605e-05 1.70839e-05 used all_to_all method: pairwise handle bytes (avg, min, max): 31677 30748 32980 buffer bytes (avg, min, max): 2892 2288 3776 setupds time 3.4194E-03 seconds 10 8 9924 730 setup h1 coarse grid, nx_crs= 2 call usrsetvert done :: usrsetvert gs_setup: 103 unique labels shared pairwise times (avg, min, max): 2.45545e-06 2.3334e-06 2.5351e-06 crystal router : 3.81156e-06 3.7179e-06 3.8942e-06 all reduce : 4.5149e-06 4.4852e-06 4.5619e-06 used all_to_all method: pairwise handle bytes (avg, min, max): 4695 4540 4900 buffer bytes (avg, min, max): 468 368 608 done :: setup h1 coarse grid 3.5807990061584860E-003 sec call usrdat3 done :: usrdat3 set initial conditions nekuic (1) for ifld 1 call nekuic for vel xyz min -2.3562 -1.0000 0.99000E+22 uvwpt min 0.99000E+22 0.99000E+22 0.99000E+22 0.0000 0.0000 PS min 0.0000 0.99000E+22 xyz max 3.9270 1.0000 -0.99000E+22 uvwpt max -0.99000E+22 -0.99000E+22 -0.99000E+22 0.0000 0.0000 PS max 0.0000 -0.99000E+22 done :: set initial conditions call userchk 0.0000E+00 NaN NaN monitor Start collecting statistics ... done :: userchk gridpoints unique/tot: 18560 26280 dofs: 18394 26280 Initialization successfully completed 0.76199E-01 sec Starting time loop ... DT/DTCFL/DTFS/DTINIT 0.100E-04 0.494-323 -0.558-261 0.100E-04 Step 1, time= 1.00000E-05, DT= 1.000E-05 Solving for fluid 1 Helmh3 fluid unconverged! 201 NaN NaN 1.0000E-08 ERROR: E-solver does not exist 0 Stop in ESOLVER ERROR: E-solver does not exist 0 Stop in ESOLVER ERROR: E-solver does not exist 0 Stop in ESOLVER ERROR: E-solver does not exist 0 Stop in ESOLVER ERROR: E-solver does not exist 0 Stop in ESOLVER ERROR: E-solver does not exist 0 Stop in ESOLVER ERROR: E-solver does not exist 0 Stop in ESOLVER ERROR: E-solver does not exist 0 Stop in ESOLVER an error occured: dying ... total elapsed time : 1.44827E-01 sec total solver time w/o IO : 0.00000E+00 sec time/timestep : 0.00000E+00 sec avg throughput per timestep : 0.00000E+00 gridpts/CPUs total max memory usage : 1.89690E-01 GB ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- -------------------------------------------------------------------------- mpiexec detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[25844,1],0] Exit code: 1 --------------------------------------------------------------------------

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Re: [Nek5000-users] Re post-processing using f0000 files
by nek5000-users＠lists.mcs.anl.gov 11 Jan '18

11 Jan '18

Hi ZJ, Yes I meant the hemi.usr case. I just looked at the usr file that you attached in earlier message, and I don’t see any discrepancies in it. It should work for your case since it only averages in z direction and since your mesh was extruded using n2to3, the element numbering should be as expected. Can you please make sure the value of nelxy i.e. number of elements in the 2D cross-section is correction. Right now it is set to 288 in the usr file. Ketan

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Сollocation of i,j,k in each spectral element
by nek5000-users＠lists.mcs.anl.gov 11 Jan '18

11 Jan '18

Hi, Neks! I am working with a complex geometry witch was built in gambit. And I want to change positions of some points in spectral elements. I've read in documentation that i,j,k,e in xm1(i,j,k,e), for example, are changed from 1 to nx1,ny1,nz1 and nelv respectively. But during my tests it's seemed that in different elements x,y,z axis not always correspond to the global coordinate system. Am I right? And how could I find out the principle of collocation of i,j,k in each spectral element? Best regards, Elizabeth

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Question about iside value
by nek5000-users＠lists.mcs.anl.gov 11 Jan '18

11 Jan '18

Hi, Neks! I am working with a complex geometry witch was built in gambit. I want to know a parameter "iside" for each of faces ( outflow, inflow and all walls) on zero step. If I ask in userbc ( in *.usr file) write "iside", I receive only iside=1, that matches inflow. It means that faces with type "wall" don't have "iside" value,am i right? And how each surface is assigned value "iside"? Best regards, Elizabeth

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Re: [Nek5000-users] Re post-processing using f0000 files
by nek5000-users＠lists.mcs.anl.gov 10 Jan '18

10 Jan '18

Hi Ketan, Do you mean the hemi.usr in NekExamples which I found is used to demonstrate particle tracking. I didn't find the interp_uvw in the code, the only one similar to that is interp_v which evaluates velocity for list of points xyz. Is that for the particles or domain mesh? ZJ

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Re: [Nek5000-users] Re post-processing using f0000 files
by nek5000-users＠lists.mcs.anl.gov 09 Jan '18

09 Jan '18

Hi ZJ, One thing to keep in mind for the averaging process is that it assumes the element numbering is lexicographic. I.e. elements are numbered sequentially in x, then y and then z. That being said, since your 2D mesh was generated in pretex, the numbering might not what the code was written for. If this is the case, a workaround would be to use the interp_uvw from the hemi case as an example to generate a set of say uniform points in your domain and then average the values at those points by using gslib_findpts_eval amd uniform weights, and writing them out to a dat file. Ketan Sent from my iPhone

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Re: [Nek5000-users] Re post-processing using f0000 files
by nek5000-users＠lists.mcs.anl.gov 09 Jan '18

09 Jan '18

Hi Marco, Please see attached rea file and usr file. Would you please help me do some changes to output the averaged velocity, rms files (means.dat or rms.dat) in the usr file. Kind regards, ZJ pipe.rea <https://drive.google.com/file/d/1oeTlJ6QgKq1EZ75w7CMBV7V1-tqDKYio/view?usp=…>

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Re: [Nek5000-users] Announcing Nek5000 17.0
by nek5000-users＠lists.mcs.anl.gov 09 Jan '18

09 Jan '18

Dear Nek Users, Please make sure to update to the latest version 17.0 (see below). Have fun! -----Original message----- > From:[email protected] <nek5000-users(a)lists.mcs.anl.gov> > Sent: Monday 18th December 2017 8:57 > To: nek5000-users(a)lists.mcs.anl.gov > Subject: [Nek5000-users] Announcing Nek5000 17.0 > > We are proud to announce that Nek5000 version 17.0 is now available for download at: > https://nek5000.mcs.anl.gov > > Please read the Release Notes carefully before using the code. > > Note, we strongly recommend to use the latest release tarball in a production environment > instead of the lastest master branch on GitHub. > > None of this incredible work would be possible without the support and contributions > of our wonderful members and community. Thank you all for your hard work! > > > Enjoy, > > The Nek Development Team > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >

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Re: [Nek5000-users] Reynolds number setting in the turbChannel example
by nek5000-users＠lists.mcs.anl.gov 09 Jan '18

09 Jan '18

Dear Marco and Paul I indeed started from the example included in the nek5000. After using .box file generate .re2 file, I just changed the Reynold's number from -10935 to -2800 and lower p26 to 0.5 in my own calculation. However, I found the p54/p55 is indeed zero, I will retry the simulation and hope this time it works. Thanks again for your help! Zhenrong JING PhD Ecole centrale de Nantes

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