May 2010 - 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

1 9

Re: [Nek5000-users] Vanishing Jacobian error description
by nek5000-users＠lists.mcs.anl.gov 10 Mar '11

10 Mar '11

Hi Paul, Here is the rea, usr, & SIZE file I am using. I ran it again without the curved side information and it worked, so I think the problem is somewhere in the curved side section of the rea. The geometry is a square base lofted into a circle in the +z direction. The mesh was generated in gambit. I've developed a matlab code that will take a mesh created in gambit and generate the required REA formatting. I have created some basic shapes to test the matlab portion and the curved side portion, and it worked in most cases (not this one yet). I'm not sure what is going on with the curved side data in this case however. Thanks for looking at this, Michael ----- Original Message ----- From: nek5000-users(a)lists.mcs.anl.gov To: "Nekton User List" <nek5000-users(a)lists.mcs.anl.gov> Sent: Tuesday, April 20, 2010 3:36:44 PM GMT -06:00 US/Canada Central Subject: Re: [Nek5000-users] Vanishing Jacobian error description Michael, The code is trying to check to ensure that the mesh is valid. Sometimes, however, there are other causes for the problem. Can you send a gzip'd rea/usr file, and I can take a look later tonight. Paul On Tue, 20 Apr 2010, nek5000-users(a)lists.mcs.anl.gov wrote: > Hi, > > I am running into an issue with 'Vanishing Jacobian'. To help understand what the problem > is, could someone explain what is meant in the error? Specifically, what it means by "Xth node" of the element. > Also, I ran into this issue when I was deforming geometries in the usr file, where one of the elements > would overlap another by mistake. However in this case I know there are no overlaps. > > Here is a portion: > > 0 ERROR: Vanishing Jacobian near 91th node of element 69. > 1.40692804605498586E-002 -7.79619559165757245E-003 > 0 xyz: 2.65874E-01 3.54498E-01 2.87050E+00 > 0 xyz: 2.07855E-01 1.77249E-01 2.87050E+00 > > > 0 ERROR: Vanishing Jacobian near 76th node of element 70. > 2.59472856644434001E-002 -2.12442422718029170E-002 > 0 xyz: 2.11655E-01 4.23310E-01 2.62500E+00 > 0 xyz: 3.54498E-01 1.77249E-01 2.87050E+00 > > Thanks for any help deciphering this error! > > - Michael > > > > > > _______________________________________________ Nek5000-users mailing list Nek5000-users(a)lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users

1 4

Visit and NEK 3D data
by nek5000-users＠lists.mcs.anl.gov 06 Jan '11

06 Jan '11

Hello all, I am running into a problem with Visit and NEK 3D data files. Visit (version 1.12.2) reads them in, but the mesh is all jumbled up. If anyone could try Visit on this file, I'd be grateful, perhaps there is some setting in Visit that I overlooked. The data file (4MB) is: http://tetra.fluid.tuwien.ac.at/fmuldoo/engineering-marangoni-flows/sim2/si… I use the following meta data file: NEK5000 version: 1.0 filetemplate: c203d.fld%02d firsttimestep: 2 numtimesteps: 1 Cheers, Frank -- Frank Herbert Muldoon, Ph.D. Mechanical Engineering Technische Universität Wien (Technical University of Vienna) Inst. f. Strömungsmechanik und Wärmeübertragung (Institute of Fluid Mechanics and Heat Transfer) Resselgasse 3 1040 Wien Tel: +4315880132232 Fax: +4315880132299 Cell:+436765203470 fmuldoo (skype) http://tetra.fluid.tuwien.ac.at/fmuldoo/public_html/webpage/frank-muldoon.h…

1 29

MHD
by nek5000-users＠lists.mcs.anl.gov 27 Jun '10

27 Jun '10

Dear Paul and Stephan, I'd like to know how to setup nek5000 to solve for MHD equations. Maybe an example? Regards, Mani chandra

1 3

Nekmerge question
by nek5000-users＠lists.mcs.anl.gov 15 Jun '10

15 Jun '10

Hello all, I know there already exists a thread having the same title dating back to November 2009, but no one has answered to it yet. I also have some question regarding nekmerge. I would like to mesh the cross-section of a cylindrical pipe. Using the cylindrical version of genbox, I obviously get into troubles as soon as I include the axis. As a consequence, I would like to merge two meshes: - a cartesian one in the vicinity of the axis - a cylindrical one for the rest of the pipe Once I genboxed the corresponding .box files, I use nekmerge and there comes my problem. I get the following error message: [loiseau@Quadstation-01 cylindre]$ ./nekmerge ascii or binary output ? (a/b): a Input new (output) file name: cylindre Input source .rea file name or press enter to continue: 1 Input source .rea file name or press enter to continue: 2 Input source .rea file name or press enter to continue: locglob: 1 1 1 324 locglob: 1 2 214 324 locglob: 2 1 289 324 locglob: 2 2 289 324 done locglob_lexico: 290 290 324 FACE ERROR: 5 3 108 5 Attached are all the .box and .rea files I have used. Could anyone give me a hint on how to solve this little problem ? Regards, Jean-Christophe ****** PARAMETERS ***** 2.60000 NEKTON VERSION 2 DIMENSIONAL RUN 103 PARAMETERS FOLLOW 1.00000 DENSITY -1000.000 VISCOS: < 0 --> Re = abs(p2) 0. BETAG 0. GTHETA 0. PGRADX 0. FLOWRATE 1.00000 RHOCP 5.00000 CONDUCT 0. QVOL 0. FINTIME 25. NSTEPS 0.500000 DT 0. IOCOMM 8.61667 IOTIME 5.0000 IOSTEP 0. EQTYPE 0. AXIS 0.200000E-01 GRID -1.00000 INTYPE 4.00000 NORDER 0.300000E-07 DIVERGENCE 0.300000E-09 HELMHOLTZ 0. NPSCAL 0.500000E-02 TOLREL 0.100000E-01 TOLABS 0.900000 COURANT 2.00000 TORDER 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. p41 1. p42 = 1 --> use Schwarz solver 1. p43 1. p44 0. p45 0. 0. 0. 0. 0. 0. 0. HISTEP 0. HISTIME 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1.00000 new file each dump (1) 4.00000 write form (0), unform(1), universal(2) 4.00000 read form (0), unform (1), universal(2) 0. 50000.0 frequency of srf dump 0. 0. 0. 0. 1.00000 p74 = verbose hmholtz0kx k 0. 517.000 76 = period of oscil, (convc. time units 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. coarse grid weighting (default=10.0) 0. 0. 0. 0 30.0000 Number of pressure sol'ns saved 0 3.00000 start saving pressure soln's after this 0 5.00000 start saving pressure soln's after this 0. which saving algorithm 1 = discard, 2= 0. p97 0. p98 3. p99 3--> dealias 0. p100 0. p101 No. of additional filter modes 1.00000 p102 Dump out divergence at each time step .001 p103 weight of stabilizing filtertime step 4 Lines of passive scalar data follows2 CONDUCT; 2RHOCP 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 12 LOGICAL SWITCHES FOLLOW T IFFLOW F IFHEAT T IFTRAN T T F F F F F F F F F IFNAV & IFADVC (convection in P.S. fields) F F T T T T T T T T T T IFTMSH (IF mesh for this field is T mesh) F IFAXIS F IFSTRS F IFMGRID F IFMODEL F IFKEPS F IFMVBD F IFCHAR 8.33333 8.33333 -3.00000 -4.33333 XFAC,YFAC,XZERO,YZERO *** MESH DATA *** 72 2 72 NEL,NDIM,NELV ELEMENT 1 [ 1a] GROUP 0 2.5000000E-01 5.0000000E-01 4.8296291E-01 2.5000000E-01 0.0000000E+00 0.0000000E+00 1.2940952E-01 8.3333336E-02 ELEMENT 2 [ 1b] GROUP 0 5.0000000E-01 6.9999999E-01 6.7614806E-01 4.8296291E-01 0.0000000E+00 0.0000000E+00 1.8117332E-01 1.2940952E-01 ELEMENT 3 [ 1c] GROUP 0 6.9999999E-01 8.0000001E-01 7.7274066E-01 6.7614806E-01 0.0000000E+00 0.0000000E+00 2.0705524E-01 1.8117332E-01 ELEMENT 4 [ 1d] GROUP 0 2.5000000E-01 4.8296291E-01 4.3301269E-01 2.5000000E-01 8.3333336E-02 1.2940952E-01 2.5000000E-01 1.6666667E-01 ELEMENT 5 [ 1e] GROUP 0 4.8296291E-01 6.7614806E-01 6.0621774E-01 4.3301269E-01 1.2940952E-01 1.8117332E-01 3.4999999E-01 2.5000000E-01 ELEMENT 6 [ 1f] GROUP 0 6.7614806E-01 7.7274066E-01 6.9282031E-01 6.0621774E-01 1.8117332E-01 2.0705524E-01 4.0000001E-01 3.4999999E-01 ELEMENT 7 [ 1g] GROUP 0 2.5000000E-01 4.3301269E-01 3.5355338E-01 2.5000000E-01 1.6666667E-01 2.5000000E-01 3.5355338E-01 2.5000000E-01 ELEMENT 8 [ 1h] GROUP 0 4.3301269E-01 6.0621774E-01 4.9497473E-01 3.5355338E-01 2.5000000E-01 3.4999999E-01 4.9497473E-01 3.5355338E-01 ELEMENT 9 [ 1i] GROUP 0 6.0621774E-01 6.9282031E-01 5.6568545E-01 4.9497473E-01 3.4999999E-01 4.0000001E-01 5.6568545E-01 4.9497473E-01 ELEMENT 10 [ 1j] GROUP 0 2.5000000E-01 3.5355338E-01 2.4999999E-01 1.6666666E-01 2.5000000E-01 3.5355338E-01 4.3301272E-01 2.5000000E-01 ELEMENT 11 [ 1k] GROUP 0 3.5355338E-01 4.9497473E-01 3.4999996E-01 2.4999999E-01 3.5355338E-01 4.9497473E-01 6.0621780E-01 4.3301272E-01 ELEMENT 12 [ 1l] GROUP 0 4.9497473E-01 5.6568545E-01 3.9999998E-01 3.4999996E-01 4.9497473E-01 5.6568545E-01 6.9282037E-01 6.0621780E-01 ELEMENT 13 [ 1m] GROUP 0 1.6666666E-01 2.4999999E-01 1.2940948E-01 8.3333313E-02 2.5000000E-01 4.3301272E-01 4.8296294E-01 2.5000000E-01 ELEMENT 14 [ 1n] GROUP 0 2.4999999E-01 3.4999996E-01 1.8117326E-01 1.2940948E-01 4.3301272E-01 6.0621780E-01 6.7614812E-01 4.8296294E-01 ELEMENT 15 [ 1o] GROUP 0 3.4999996E-01 3.9999998E-01 2.0705517E-01 1.8117326E-01 6.0621780E-01 6.9282037E-01 7.7274072E-01 6.7614812E-01 ELEMENT 16 [ 1p] GROUP 0 8.3333313E-02 1.2940948E-01 0.0000000E+00 0.0000000E+00 2.5000000E-01 4.8296294E-01 5.0000000E-01 2.5000000E-01 ELEMENT 17 [ 1q] GROUP 0 1.2940948E-01 1.8117326E-01 0.0000000E+00 0.0000000E+00 4.8296294E-01 6.7614812E-01 6.9999999E-01 5.0000000E-01 ELEMENT 18 [ 1r] GROUP 0 1.8117326E-01 2.0705517E-01 0.0000000E+00 0.0000000E+00 6.7614812E-01 7.7274072E-01 8.0000001E-01 6.9999999E-01 ELEMENT 19 [ 1s] GROUP 0 0.0000000E+00 0.0000000E+00 -1.2940963E-01 -8.3333373E-02 2.5000000E-01 5.0000000E-01 4.8296288E-01 2.5000000E-01 ELEMENT 20 [ 1t] GROUP 0 0.0000000E+00 0.0000000E+00 -1.8117347E-01 -1.2940963E-01 5.0000000E-01 6.9999999E-01 6.7614800E-01 4.8296288E-01 ELEMENT 21 [ 1u] GROUP 0 0.0000000E+00 0.0000000E+00 -2.0705540E-01 -1.8117347E-01 6.9999999E-01 8.0000001E-01 7.7274060E-01 6.7614800E-01 ELEMENT 22 [ 1v] GROUP 0 -8.3333373E-02 -1.2940963E-01 -2.5000003E-01 -1.6666669E-01 2.5000000E-01 4.8296288E-01 4.3301269E-01 2.5000000E-01 ELEMENT 23 [ 1w] GROUP 0 -1.2940963E-01 -1.8117347E-01 -3.5000002E-01 -2.5000003E-01 4.8296288E-01 6.7614800E-01 6.0621774E-01 4.3301269E-01 ELEMENT 24 [ 1x] GROUP 0 -1.8117347E-01 -2.0705540E-01 -4.0000007E-01 -3.5000002E-01 6.7614800E-01 7.7274060E-01 6.9282031E-01 6.0621774E-01 ELEMENT 25 [ 1y] GROUP 0 -1.6666669E-01 -2.5000003E-01 -3.5355338E-01 -2.5000000E-01 2.5000000E-01 4.3301269E-01 3.5355338E-01 2.5000000E-01 ELEMENT 26 [ 1z] GROUP 0 -2.5000003E-01 -3.5000002E-01 -4.9497473E-01 -3.5355338E-01 4.3301269E-01 6.0621774E-01 4.9497473E-01 3.5355338E-01 ELEMENT 27 [ 1A] GROUP 0 -3.5000002E-01 -4.0000007E-01 -5.6568545E-01 -4.9497473E-01 6.0621774E-01 6.9282031E-01 5.6568545E-01 4.9497473E-01 ELEMENT 28 [ 1B] GROUP 0 -2.5000000E-01 -3.5355338E-01 -4.3301275E-01 -2.5000000E-01 2.5000000E-01 3.5355338E-01 2.4999991E-01 1.6666663E-01 ELEMENT 29 [ 1C] GROUP 0 -3.5355338E-01 -4.9497473E-01 -6.0621786E-01 -4.3301275E-01 3.5355338E-01 4.9497473E-01 3.4999987E-01 2.4999991E-01 ELEMENT 30 [ 1D] GROUP 0 -4.9497473E-01 -5.6568545E-01 -6.9282043E-01 -6.0621786E-01 4.9497473E-01 5.6568545E-01 3.9999986E-01 3.4999987E-01 ELEMENT 31 [ 1E] GROUP 0 -2.5000000E-01 -4.3301275E-01 -4.8296294E-01 -2.5000000E-01 1.6666663E-01 2.4999991E-01 1.2940946E-01 8.3333313E-02 ELEMENT 32 [ 1F] GROUP 0 -4.3301275E-01 -6.0621786E-01 -6.7614812E-01 -4.8296294E-01 2.4999991E-01 3.4999987E-01 1.8117325E-01 1.2940946E-01 ELEMENT 33 [ 1G] GROUP 0 -6.0621786E-01 -6.9282043E-01 -7.7274072E-01 -6.7614812E-01 3.4999987E-01 3.9999986E-01 2.0705514E-01 1.8117325E-01 ELEMENT 34 [ 1H] GROUP 0 -2.5000000E-01 -4.8296294E-01 -5.0000000E-01 -2.5000000E-01 8.3333313E-02 1.2940946E-01 0.0000000E+00 0.0000000E+00 ELEMENT 35 [ 1I] GROUP 0 -4.8296294E-01 -6.7614812E-01 -6.9999999E-01 -5.0000000E-01 1.2940946E-01 1.8117325E-01 0.0000000E+00 0.0000000E+00 ELEMENT 36 [ 1J] GROUP 0 -6.7614812E-01 -7.7274072E-01 -8.0000001E-01 -6.9999999E-01 1.8117325E-01 2.0705514E-01 0.0000000E+00 0.0000000E+00 ELEMENT 37 [ 1K] GROUP 0 -2.5000000E-01 -5.0000000E-01 -4.8296288E-01 -2.5000000E-01 0.0000000E+00 0.0000000E+00 -1.2940966E-01 -8.3333373E-02 ELEMENT 38 [ 1L] GROUP 0 -5.0000000E-01 -6.9999999E-01 -6.7614800E-01 -4.8296288E-01 0.0000000E+00 0.0000000E+00 -1.8117352E-01 -1.2940966E-01 ELEMENT 39 [ 1M] GROUP 0 -6.9999999E-01 -8.0000001E-01 -7.7274060E-01 -6.7614800E-01 0.0000000E+00 0.0000000E+00 -2.0705545E-01 -1.8117352E-01 ELEMENT 40 [ 1N] GROUP 0 -2.5000000E-01 -4.8296288E-01 -4.3301257E-01 -2.5000000E-01 -8.3333373E-02 -1.2940966E-01 -2.5000021E-01 -1.6666675E-01 ELEMENT 41 [ 1O] GROUP 0 -4.8296288E-01 -6.7614800E-01 -6.0621762E-01 -4.3301257E-01 -1.2940966E-01 -1.8117352E-01 -3.5000029E-01 -2.5000021E-01 ELEMENT 42 [ 1P] GROUP 0 -6.7614800E-01 -7.7274060E-01 -6.9282013E-01 -6.0621762E-01 -1.8117352E-01 -2.0705545E-01 -4.0000033E-01 -3.5000029E-01 ELEMENT 43 [ 1Q] GROUP 0 -2.5000000E-01 -4.3301257E-01 -3.5355332E-01 -2.5000000E-01 -1.6666675E-01 -2.5000021E-01 -3.5355344E-01 -2.5000000E-01 ELEMENT 44 [ 1R] GROUP 0 -4.3301257E-01 -6.0621762E-01 -4.9497464E-01 -3.5355332E-01 -2.5000021E-01 -3.5000029E-01 -4.9497482E-01 -3.5355344E-01 ELEMENT 45 [ 1S] GROUP 0 -6.0621762E-01 -6.9282013E-01 -5.6568533E-01 -4.9497464E-01 -3.5000029E-01 -4.0000033E-01 -5.6568551E-01 -4.9497482E-01 ELEMENT 46 [ 1T] GROUP 0 -2.5000000E-01 -3.5355332E-01 -2.4999996E-01 -1.6666663E-01 -2.5000000E-01 -3.5355344E-01 -4.3301272E-01 -2.5000000E-01 ELEMENT 47 [ 1U] GROUP 0 -3.5355332E-01 -4.9497464E-01 -3.4999993E-01 -2.4999996E-01 -3.5355344E-01 -4.9497482E-01 -6.0621780E-01 -4.3301272E-01 ELEMENT 48 [ 1V] GROUP 0 -4.9497464E-01 -5.6568533E-01 -3.9999995E-01 -3.4999993E-01 -4.9497482E-01 -5.6568551E-01 -6.9282037E-01 -6.0621780E-01 ELEMENT 49 [ 1W] GROUP 0 -1.6666663E-01 -2.4999996E-01 -1.2940927E-01 -8.3333254E-02 -2.5000000E-01 -4.3301272E-01 -4.8296300E-01 -2.5000000E-01 ELEMENT 50 [ 1X] GROUP 0 -2.4999996E-01 -3.4999993E-01 -1.8117297E-01 -1.2940927E-01 -4.3301272E-01 -6.0621780E-01 -6.7614818E-01 -4.8296300E-01 ELEMENT 51 [ 1Y] GROUP 0 -3.4999993E-01 -3.9999995E-01 -2.0705484E-01 -1.8117297E-01 -6.0621780E-01 -6.9282037E-01 -7.7274078E-01 -6.7614818E-01 ELEMENT 52 [ 1Z] GROUP 0 -8.3333254E-02 -1.2940927E-01 0.0000000E+00 0.0000000E+00 -2.5000000E-01 -4.8296300E-01 -5.0000000E-01 -2.5000000E-01 ELEMENT 53 [ 1a] GROUP 0 -1.2940927E-01 -1.8117297E-01 0.0000000E+00 0.0000000E+00 -4.8296300E-01 -6.7614818E-01 -6.9999999E-01 -5.0000000E-01 ELEMENT 54 [ 1b] GROUP 0 -1.8117297E-01 -2.0705484E-01 0.0000000E+00 0.0000000E+00 -6.7614818E-01 -7.7274078E-01 -8.0000001E-01 -6.9999999E-01 ELEMENT 55 [ 1c] GROUP 0 0.0000000E+00 0.0000000E+00 1.2940973E-01 8.3333373E-02 -2.5000000E-01 -5.0000000E-01 -4.8296285E-01 -2.5000000E-01 ELEMENT 56 [ 1d] GROUP 0 0.0000000E+00 0.0000000E+00 1.8117362E-01 1.2940973E-01 -5.0000000E-01 -6.9999999E-01 -6.7614800E-01 -4.8296285E-01 ELEMENT 57 [ 1e] GROUP 0 0.0000000E+00 0.0000000E+00 2.0705557E-01 1.8117362E-01 -6.9999999E-01 -8.0000001E-01 -7.7274054E-01 -6.7614800E-01 ELEMENT 58 [ 1f] GROUP 0 8.3333373E-02 1.2940973E-01 2.5000018E-01 1.6666675E-01 -2.5000000E-01 -4.8296285E-01 -4.3301260E-01 -2.5000000E-01 ELEMENT 59 [ 1g] GROUP 0 1.2940973E-01 1.8117362E-01 3.5000023E-01 2.5000018E-01 -4.8296285E-01 -6.7614800E-01 -6.0621762E-01 -4.3301260E-01 ELEMENT 60 [ 1h] GROUP 0 1.8117362E-01 2.0705557E-01 4.0000030E-01 3.5000023E-01 -6.7614800E-01 -7.7274054E-01 -6.9282019E-01 -6.0621762E-01 ELEMENT 61 [ 1i] GROUP 0 1.6666675E-01 2.5000018E-01 3.5355350E-01 2.5000000E-01 -2.5000000E-01 -4.3301260E-01 -3.5355327E-01 -2.5000000E-01 ELEMENT 62 [ 1j] GROUP 0 2.5000018E-01 3.5000023E-01 4.9497491E-01 3.5355350E-01 -4.3301260E-01 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-3.9999983E-01 -2.0705508E-01 -1.8117318E-01 ELEMENT 70 [ 1r] GROUP 0 2.5000000E-01 4.8296294E-01 5.0000000E-01 2.5000000E-01 -8.3333254E-02 -1.2940942E-01 0.0000000E+00 0.0000000E+00 ELEMENT 71 [ 1s] GROUP 0 4.8296294E-01 6.7614812E-01 6.9999999E-01 5.0000000E-01 -1.2940942E-01 -1.8117318E-01 0.0000000E+00 0.0000000E+00 ELEMENT 72 [ 1t] GROUP 0 6.7614812E-01 7.7274072E-01 8.0000001E-01 6.9999999E-01 -1.8117318E-01 -2.0705508E-01 0.0000000E+00 0.0000000E+00 ***** CURVED SIDE DATA ***** 72 Curved sides follow IEDGE,IEL,CURVE(I),I=1,5, CCURVE 2 2 0.700000 0.00000 0.00000 0.00000 0.00000 C 2 3 0.800000 0.00000 0.00000 0.00000 0.00000 C 4 3 -0.700000 0.00000 0.00000 0.00000 0.00000 C 2 5 0.700000 0.00000 0.00000 0.00000 0.00000 C 2 6 0.800000 0.00000 0.00000 0.00000 0.00000 C 4 6 -0.700000 0.00000 0.00000 0.00000 0.00000 C 2 8 0.700000 0.00000 0.00000 0.00000 0.00000 C 2 9 0.800000 0.00000 0.00000 0.00000 0.00000 C 4 9 -0.700000 0.00000 0.00000 0.00000 0.00000 C 2 11 0.700000 0.00000 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1.000000 0.000000 0.000000 0.000000 E 72 4 71.00000 2.000000 0.000000 0.000000 0.000000 ****** PARAMETERS ***** 2.60000 NEKTON VERSION 2 DIMENSIONAL RUN 103 PARAMETERS FOLLOW 1.00000 DENSITY -1000.000 VISCOS: < 0 --> Re = abs(p2) 0. BETAG 0. GTHETA 0. PGRADX 0. FLOWRATE 1.00000 RHOCP 5.00000 CONDUCT 0. QVOL 0. FINTIME 25. NSTEPS 0.500000 DT 0. IOCOMM 8.61667 IOTIME 5.0000 IOSTEP 0. EQTYPE 0. AXIS 0.200000E-01 GRID -1.00000 INTYPE 4.00000 NORDER 0.300000E-07 DIVERGENCE 0.300000E-09 HELMHOLTZ 0. NPSCAL 0.500000E-02 TOLREL 0.100000E-01 TOLABS 0.900000 COURANT 2.00000 TORDER 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. p41 1. p42 = 1 --> use Schwarz solver 1. p43 1. p44 0. p45 0. 0. 0. 0. 0. 0. 0. HISTEP 0. HISTIME 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1.00000 new file each dump (1) 4.00000 write form (0), unform(1), universal(2) 4.00000 read form (0), unform (1), universal(2) 0. 50000.0 frequency of srf dump 0. 0. 0. 0. 1.00000 p74 = verbose hmholtz0kx k 0. 517.000 76 = period of oscil, (convc. time units 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. coarse grid weighting (default=10.0) 0. 0. 0. 0 30.0000 Number of pressure sol'ns saved 0 3.00000 start saving pressure soln's after this 0 5.00000 start saving pressure soln's after this 0. which saving algorithm 1 = discard, 2= 0. p97 0. p98 3. p99 3--> dealias 0. p100 0. p101 No. of additional filter modes 1.00000 p102 Dump out divergence at each time step .001 p103 weight of stabilizing filtertime step 4 Lines of passive scalar data follows2 CONDUCT; 2RHOCP 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 12 LOGICAL SWITCHES FOLLOW T IFFLOW F IFHEAT T IFTRAN T T F F F F F F F F F IFNAV & IFADVC (convection in P.S. fields) F F T T T T T T T T T T IFTMSH (IF mesh for this field is T mesh) F IFAXIS F IFSTRS F IFMGRID F IFMODEL F IFKEPS F IFMVBD F IFCHAR 8.33333 8.33333 -3.00000 -4.33333 XFAC,YFAC,XZERO,YZERO *** MESH DATA *** 9 2 9 NEL,NDIM,NELV ELEMENT 1 [ 1a] GROUP 0 -0.500000 -0.166667 -0.166667 -0.500000 -0.500000 -0.500000 -0.166667 -0.166667 ELEMENT 2 [ 1b] GROUP 0 -0.166667 0.166667 0.166667 -0.166667 -0.500000 -0.500000 -0.166667 -0.166667 ELEMENT 3 [ 1c] GROUP 0 0.166667 0.500000 0.500000 0.166667 -0.500000 -0.500000 -0.166667 -0.166667 ELEMENT 4 [ 1d] GROUP 0 -0.500000 -0.166667 -0.166667 -0.500000 -0.166667 -0.166667 0.166667 0.166667 ELEMENT 5 [ 1e] GROUP 0 -0.166667 0.166667 0.166667 -0.166667 -0.166667 -0.166667 0.166667 0.166667 ELEMENT 6 [ 1f] GROUP 0 0.166667 0.500000 0.500000 0.166667 -0.166667 -0.166667 0.166667 0.166667 ELEMENT 7 [ 1g] GROUP 0 -0.500000 -0.166667 -0.166667 -0.500000 0.166667 0.166667 0.500000 0.500000 ELEMENT 8 [ 1h] GROUP 0 -0.166667 0.166667 0.166667 -0.166667 0.166667 0.166667 0.500000 0.500000 ELEMENT 9 [ 1i] GROUP 0 0.166667 0.500000 0.500000 0.166667 0.166667 0.166667 0.500000 0.500000 ***** CURVED SIDE DATA ***** 0 Curved sides follow IEDGE,IEL,CURVE(I),I=1,5, CCURVE ***** BOUNDARY CONDITIONS ***** ***** FLUID BOUNDARY CONDITIONS ***** E 1 1 0.000000 0.000000 0.000000 0.000000 0.000000 E 1 2 2.000000 4.000000 0.000000 0.000000 0.000000 E 1 3 4.000000 1.000000 0.000000 0.000000 0.000000 E 1 4 0.000000 0.000000 0.000000 0.000000 0.000000 E 2 1 0.000000 0.000000 0.000000 0.000000 0.000000 E 2 2 3.000000 4.000000 0.000000 0.000000 0.000000 E 2 3 5.000000 1.000000 0.000000 0.000000 0.000000 E 2 4 1.000000 2.000000 0.000000 0.000000 0.000000 E 3 1 0.000000 0.000000 0.000000 0.000000 0.000000 E 3 2 0.000000 0.000000 0.000000 0.000000 0.000000 E 3 3 6.000000 1.000000 0.000000 0.000000 0.000000 E 3 4 2.000000 2.000000 0.000000 0.000000 0.000000 E 4 1 1.000000 3.000000 0.000000 0.000000 0.000000 E 4 2 5.000000 4.000000 0.000000 0.000000 0.000000 E 4 3 7.000000 1.000000 0.000000 0.000000 0.000000 E 4 4 0.000000 0.000000 0.000000 0.000000 0.000000 E 5 1 2.000000 3.000000 0.000000 0.000000 0.000000 E 5 2 6.000000 4.000000 0.000000 0.000000 0.000000 E 5 3 8.000000 1.000000 0.000000 0.000000 0.000000 E 5 4 4.000000 2.000000 0.000000 0.000000 0.000000 E 6 1 3.000000 3.000000 0.000000 0.000000 0.000000 E 6 2 0.000000 0.000000 0.000000 0.000000 0.000000 E 6 3 9.000000 1.000000 0.000000 0.000000 0.000000 E 6 4 5.000000 2.000000 0.000000 0.000000 0.000000 E 7 1 4.000000 3.000000 0.000000 0.000000 0.000000 E 7 2 8.000000 4.000000 0.000000 0.000000 0.000000 E 7 3 0.000000 0.000000 0.000000 0.000000 0.000000 E 7 4 0.000000 0.000000 0.000000 0.000000 0.000000 E 8 1 5.000000 3.000000 0.000000 0.000000 0.000000 E 8 2 9.000000 4.000000 0.000000 0.000000 0.000000 E 8 3 0.000000 0.000000 0.000000 0.000000 0.000000 E 8 4 7.000000 2.000000 0.000000 0.000000 0.000000 E 9 1 6.000000 3.000000 0.000000 0.000000 0.000000 E 9 2 0.000000 0.000000 0.000000 0.000000 0.000000 E 9 3 0.000000 0.000000 0.000000 0.000000 0.000000 E 9 4 8.000000 2.000000 0.000000 0.000000 0.000000 ***** NO THERMAL BOUNDARY CONDITIONS ***** 0 PRESOLVE/RESTART OPTIONS ***** 7 INITIAL CONDITIONS ***** C Default C Default C Default C Default C Default C Default C Default ***** DRIVE FORCE DATA ***** BODY FORCE, FLOW, Q 4 Lines of Drive force data follow C C C C ***** Variable Property Data ***** Overrrides Parameter data. 1 Lines follow. 0 PACKETS OF DATA FOLLOW ***** HISTORY AND INTEGRAL DATA ***** 0 POINTS. Hcode, I,J,H,IEL ***** OUTPUT FIELD SPECIFICATION ***** 6 SPECIFICATIONS FOLLOW T COORDINATES T VELOCITY T PRESSURE F TEMPERATURE F TEMPERATURE GRADIENT 0 PASSIVE SCALARS ***** OBJECT SPECIFICATION ***** 0 Surface Objects 0 Volume Objects 0 Edge Objects 0 Point Objects cylindre.rea -2 1 # # # Box 1 -3 -3 -.5 .5 1.0 -.5 .5 1.0 E ,E ,E ,E , , cylindre.rea 2 1 # # # Y 3 -24 1 0 0 bocc .25 .5 .7 .8 0 1 1 E ,W ,E ,E ,

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genmap
by nek5000-users＠lists.mcs.anl.gov 13 Jun '10

13 Jun '10

Hi Neks, Is anyone having trouble with genmap in the latest build (519)? I believe I last used genmap in version 503 without problems, but now when I try to run it, it immediately says "Killed". Thanks, David

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NEKTON and Gambit
by nek5000-users＠lists.mcs.anl.gov 03 Jun '10

03 Jun '10

Hello all, I notice that Fluent's grid generator Gambit writes out meshes in NEKTON format. However, from looking at the (ASCI) file it write out, it doesn't seem to be related to the structure the NEK5000 is expecting. Does anyone know if it is at all possible to get a mesh from Gambit into a format that NEK5000 can use? Cheers, Frank -- Frank Herbert Muldoon, Ph.D. Mechanical Engineering Technische Universität Wien (Technical University of Vienna) Inst. f. Strömungsmechanik und Wärmeübertragung (Institute of Fluid Mechanics and Heat Transfer) Resselgasse 3 1040 Wien Tel: +4315880132232 Fax: +4315880132299 Cell:+436765203470 fmuldoo (skype) http://tetra.fluid.tuwien.ac.at/fmuldoo/public_html/webpage/frank-muldoon.h…

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mpich2? (fwd)
by nek5000-users＠lists.mcs.anl.gov 27 May '10

27 May '10

Hi Stefan, Any ideas? Thanks! Paul ---------- Forwarded message ---------- Date: Thu, 27 May 2010 16:15:14 -0400 (EDT) From: Tamay Ozgokmen <tozgokmen(a)rsmas.miami.edu> To: Zongjun Hu <zhu(a)med.miami.edu> Cc: fischer(a)mcs.anl.gov Subject: mpich2? Hi Paul, I installed latest code on one of UM's linux clusters but have trouble to get p4c running; it gets stuck after the prelims. See below. Any ideas...? (I will be out of touch for a few hours, unfortunately, a later meeting...) Tamay gs_setup: 379187 unique labels shared pairwise times (avg, min, max): 0.0235193 0.0224905 0.043084 crystal router : 0.00944349 0.00717771 0.029574 used all_to_all method: crystal router setupds time 2.5930E+00 seconds 3 4 2545856 131072 setvert3d: 6 8149312 16537920 8149312 8149312 call usrsetvert done :: usrsetvert gs_setup: 1062197 unique labels shared pairwise times (avg, min, max): 0.0277191 0.0266448 0.0471066 crystal router : 0.0466603 0.0462395 0.0471185 used all_to_all method: pairwise setupds time 5.2800E+00 seconds 4 6 8149312 131072 setup h1 coarse grid, nx_crs= 2 call usrsetvert done :: usrsetvert gs_setup: 40385 unique labels shared pairwise times (avg, min, max): 0.000733222 0.00068059 0.000779104 crystal router : 0.00111822 0.00108392 0.00117099 all reduce : 0.0248416 0.0245946 0.0251968 used all_to_all method: pairwise gs_setup: 40385 unique labels shared pairwise times (avg, min, max): 0.000738662 0.000688004 0.000781512 crystal router : 0.00110533 0.00107729 0.00113969 all reduce : 0.0281804 0.0244667 0.0450669 used all_to_all method: pairwise rank 87 in job 1 n0422_55429 caused collective abort of all ranks exit status of rank 87: killed by signal 9 rank 88 in job 1 n0422_55429 caused collective abort of all ranks exit status of rank 88: killed by signal 9 rank 12 in job 1 n0422_55429 caused collective abort of all ranks exit status of rank 12: killed by signal 9 rank 50 in job 1 n0422_55429 caused collective abort of all ranks exit status of rank 50: killed by signal 9 rank 16 in job 1 n0422_55429 caused collective abort of all ranks exit status of rank 16: killed by signal 9 Job /share/apps/lsf/7.0/linux2.6-glibc2.3-x86_64/bin/mpich2_wrapper ./nek5000

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Qustions about averaging for a 2D case
by nek5000-users＠lists.mcs.anl.gov 27 May '10

27 May '10

Hi, I am running a 2D DNS simulation of backward facing step combustor with a microjet. The microjet is placed on the step at 0.5H from the bottom wall. The incoming velocity is U_o = 12.5 m/s and the microjet velocity is 25 m/s. After running the case for 10 flow throughs, I started averaging over the next 8 flow throughs. But the results for averaging don't exactly look right. The geometry used and the averaged x-velocity colorfill contours can be seen in the image at link below. http://www2.uic.edu/~hkanch1/avg_mj10000.bmp I have tried averaging twice, once over 5 flow throughs and other over 8 flow throughs. Both time getting similar results. Here are the parameters that I am setting in the .rea file. ************************************************************************ 103 Parameters from file:/home/harish/nek5_examples/2D_bfs/mj_2d/mj1.rea 1 1.00000 DENSITY 2 1.556e-5 VISCOS 4 1.00000 GTHETA 7 1.00000 RHOCP 8 0.100000E-01 CONDUCT 11 128000.00 NSTEPS 12 -0.0000010 DT 15 128000 IOSTEP 18 0.500000E-01 GRID 19 -1.00000 INTYPE 20 5.00000 NORDER 21 1.000000E-07 DIVERGENCE 22 1.000000E-09 HELMHOLTZ 24 0.100000E-01 TOLREL 25 0.100000E-01 TOLABS 26 2.000000 COURANT 27 3.00000 TORDER 28 0.000000E+00 49 0.000000E+00 66 4.00000 write form (0), unform(1), universal(2) 67 4.00000 read form (0), unform (1), universal(2) 93 20.00000E+00 Number of pressure sol'ns saved 94 5.000000E+00 start saving pressure soln's after this 95 5.000000E+00 start saving pressure soln's after this 99 3.00000 p99 = 3 --> dealias turned on 103 0.01 103 filter weight IFTRAN = T IFFLOW = T IFHEAT = F IFSPLIT = T IFLOMACH = F IFUSERVP = F IFUSERMV = F IFSTRS = F IFCHAR = T IFCYCLIC = F IFAXIS = F IFMVBD = F IFMELT = F IFMODEL = F IFKEPS = F IFMOAB = F IFSYNC = T ************************************************************************ At the outflow, I am using the "fill_div(usrdiv)" subroutine provided in the "peris.usr" example. Is it possible the value of "vnmo_desire = 5.0", that I set, is too high? I choose this value because at lower values the simulation would blow up. Is there a way to calculate this value based on incoming velocity? Thanks for all the help, Harish

1 0

MHD in a sphere
by nek5000-users＠lists.mcs.anl.gov 26 May '10

26 May '10

Dear Aleks Saw your recent post that you would supply an example for MHD. I am looking to solve the MHD problem in a sphere (velocity, temperature and magnetic induction equations). Also need to set the boundary conditions for the electric current (conducting/insulating). Any help would be great.. many thanks Binod _________________________________________________________________ http://clk.atdmt.com/UKM/go/195013117/direct/01/

1 1