January 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] 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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Postx
by nek5000-users＠lists.mcs.anl.gov 02 Feb '11

02 Feb '11

Hello Neks, I am trying to post process the fld files using postx to generate a uniform xy grid of passive scalar data. During post processing the top half of the circular cross-section is cut-off (its a cylindrical domain with aspect ratio of 10 i.e radius to depth). The output file generated has only zeros in it. I have checked the input file and it has information of the entire domain. Any idea if i need to do something differently. Thanks, Himanshu

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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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viscous term
by nek5000-users＠lists.mcs.anl.gov 19 Jan '11

19 Jan '11

Hi, In an simulation with the LowMach number formulation I need to compute the term : Laplacian(U) + 1/3 grad ( div(U) ) Is it stored somewhere ( BFX,BFY,BFZ ??? )? Moreover, since i need it anyway during postprocessing, which is the most efficient way to extract it? Thank you. francesco

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Re: [Nek5000-users] Nek5000 and Non-Newtonian Fluids
by nek5000-users＠lists.mcs.anl.gov 18 Jan '11

18 Jan '11

Paul, I switched this to the nek5000-users channel in case we discuss some thing relevant to others. For the Bingham model, it seems that all I need is to calculate the second invariant of the strain rate tensor, which is then used to calculate the time-varying apparent viscosity. I suspect the routine building-blocks for generating this tensor are already in the nek distribution. If so, could you point me in that direction? Once those routines are in order, all the calculation will be directed out of uservp, correct? Thanks. --Mike On Jan 14, 2011, at 7:27 AM, Paul Fischer wrote: > Hi Mike, > > [...] > The "peris" case uses the stress formulation, as do the "fs" > cases. These have the correct SiZE files (resp. for 3D and 2D) > and flags in the .rea file, save that you would set "IFMVBD" > to false, since you don't want moving boundaries. > > [...] > The code was used > for a lot of non-Newtonian stuff by Lee Ho and Einar, however, > so it has been exercised significantly in the past. > [...]

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computing grad(T) in NEK5000
by nek5000-users＠lists.mcs.anl.gov 18 Jan '11

18 Jan '11

Dear Paul, I want to compute grad(Temp_field) for Rayleigh-Benard convection simulation. I found two functions in navier1.f, "opgrad" and "opgradt" which compute grad(scalar_field). Which one of these functions should I use? Please help. with regards, Supriyo -- Dr. Supriyo Paul Senior Project Scientist Department of Physics Indian Institute of Technology Kanpur 208 016 INDIA

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Compilation issue
by nek5000-users＠lists.mcs.anl.gov 07 Jan '11

07 Jan '11

Dear all, this morning I checked out the latest revision of nek5000 (revision 620). I am trying right now to compile a new case and I have some compiling issues.Therefore I tried to compile the same case I compiled successfully this morning before the check out and I have the same issue. I send you the file with the compiler message. Best regards, Andrea.

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