December 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

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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] 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

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lambda2
by nek5000-users＠lists.mcs.anl.gov 28 Jan '11

28 Jan '11

dear neks, in the source file postpro.f i found the following subroutine: subroutine lambda2(l2) c c Generate Lambda-2 vortex of Jeong & Hussein, JFM '95 c ... but it is not used in the code and i wanted calculate it for some visualizations. may you can explain me how i can use it. because i tried just to call it in the usrchk subroutine but then i get an error message (segmentation fault...). best, fred

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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…

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Post-Processing from avg_all files using Nek / Visit
by nek5000-users＠lists.mcs.anl.gov 31 Dec '10

31 Dec '10

Hi, I would like to post-process quantities from avg_all files (rms, rm2, avg). Particularly I am looking at line plots (mainly) or contours on a plane. I had a question regarding the approach that I might be taking.. If I load the files, say rmsblah.f0000* into nek using the load subroutine and fill the ux,uy,uz arrays with that of <u^2>, <v^2>, <w^2> and call hpts(), how would the interpolation work ? Would it interpolate <u^2> with the interpolation that is used for velocities ?. The other option would be to do a line plot from Visit and export it to a text file. Also, I am not sure how Visit interpolates. Which is more likely to be accurate ? Regards Shriram

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mixed Velocity BC's
by nek5000-users＠lists.mcs.anl.gov 31 Dec '10

31 Dec '10

Howdy Neks, Has anyone tried or know how to implement a mixed velocity BC? Such as v=w=0 and du/dy=const? Thanks Andrew -- Andrew Duggleby, Ph.D. '01 Assistant Professor Department of Mechanical Engineering Texas A&M University College Station, TX 77843-3123 109 Engineering Physics Building http://www2.mengr.tamu.edu/FacultyProfiles/facultyinformation.asp?LastName=… (979) 862-7835

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Re: [Nek5000-users] Nek5000 example errors
by nek5000-users＠lists.mcs.anl.gov 29 Dec '10

29 Dec '10

John, Am cc'g this to the users list in case anyone else has seen this problem w/ gfortran / gcc. Paul On Wed, 29 Dec 2010, John Akerley wrote: > Yes, also using gcc (both version 4.4). I did switch IFMPI to false. > Also, I re-downloaded the code yesterday due to other problems, so I > assume it's the latest version. I got a similar error when trying the > turbChannel example. The compilation is successful, but after trying > either nek or nekb, I get an error. Attached is makenek. > > Thanks, > > John > > > > On Wed, Dec 29, 2010 at 12:30 PM, Paul Fischer <fischer(a)mcs.anl.gov> wrote: >> >> Hi John, >> >> Are you also using gcc ? >> Did you switch IFMPI to false in makenek ? >> >> Did you just recently download the code ? (The test >> that I just made was done by downloading the current >> code after your previous email.) >> >> Confused, but certain we'll get to the bottom of this... >> >> Paul >> >> >> >> >> On Wed, 29 Dec 2010, John Akerley wrote: >> >>> Paul, >>> >>> I tried this and still received "Right-handed check failed for �256 >>> elements. �Exiting in routine VERRHE" after using grep -i err logfile >>> | tail command. �I am using the gfortran compiler (no mpi). �The >>> machine is a 64 bit with Redhat. >>> >>> On Wed, Dec 29, 2010 at 12:21 PM, Paul Fischer <fischer(a)mcs.anl.gov> >>> wrote: >>>> >>>> Hi John, >>>> >>>> I just tried this myself and it worked ok. >>>> >>>> Can you try the following: >>>> >>>> makenek clean >>>> makenek eddy_uv >>>> nekb eddy_uv >>>> >>>> (Note, I've posted a new manual online, accessible via the >>>> wiki or directly via: >>>> >>>> www.mcs.anl.gov/~fischer/new.pdf >>>> >>>> ... and this will be continually updated.) >>>> >>>> The "nekb" script is in nek5_svn/trunk/tools/scripts >>>> >>>> >>>> Please let me know if the above works. � Q: what compiler >>>> are you using ? >>>> >>>> Paul >>>> >>>> >>>> On Wed, 29 Dec 2010, John Akerley wrote: >>>> >>>>> Hi Paul, >>>>> >>>>> I have nek5000 installed and running on our linux machine, but I am >>>>> running into the same error when trying a few of the examples. �The >>>>> logfile is created, but when checking the error I get "Right-handed >>>>> check failed for �256 elements. �Exiting in routine VERRHE". �Do you >>>>> have a solution? �I attached the logfile. >>>>> >>>>> Thanks, >>>>> >>>>> John Akerley >>>>> >>>> >> >

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Re: [Nek5000-users] Question about running error
by nek5000-users＠lists.mcs.anl.gov 29 Dec '10

29 Dec '10

Dear Albert, It looks like your case ran successfully. (grep tep *.out shows this) You can visualize the results using VisIt. There is also a way to visualize using postx -- please see the (under construction) manual: www.mcs.anl.gov/~fischer/new.pdf on how to build and run postx. At present, you would need to rerun the turbChannel case with subroutine userdat2 : : param(66)=4 param(67)=4 and with these parameters set to 4 in the .rea file. This requirement will go away within a couple of weeks once I convert postx to support the new default output file format (.f00000 vs .fld00). I'm hoping we'll soon have a similar "get started" section about using VisIt in the manual. VisIt it much better than postx for 3D analysis. Paul

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