May 2010 - Nek5000-users - mailman3.cels.anl.gov

creating circular mesh
by nek5000-users＠lists.mcs.anl.gov 12 May '10

12 May '10

Hello all, Is there anyone out there who has a script/input for meshing a circular pipe/cylinder using "pretex"? 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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cylindrical mesh & cyl_box
by nek5000-users＠lists.mcs.anl.gov 11 May '10

11 May '10

Hello all, I notice that there is a routine "cyl_box" in "genbox.f". It seems that this routine generates meshes for cylindrical geometries. Does anyone out there use this routine and/or have any documentation on it? 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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perturbing interior variables
by nek5000-users＠lists.mcs.anl.gov 11 May '10

11 May '10

Hello all, I am trying to perturb the temperature in a small part of the flow. However, I only wish to perturb in the interior and not on a boundary. I have the following in "userchk". If I instead looped from "k=1,nz1" instead of "k=2,nz1-1", would this change the BC's? The general question would be, does changing uvw & T in "userchk" change BC's or does "userbc" override what is done in "userchk"? Cheers, Frank do 100 iel=1,nelv do 100 k=2,nz1-1 do 100 j=2,ny1-1 do 100 i=2,nx1-1 if(((xm1(i,j,k,iel)-1.1)**2 & + (ym1(i,j,k,iel)-1.1)**2 & + (zm1(i,j,k,iel)-.45)**2)**.5.le..25)then t(i,j,k,iel)=.99*t(i,j,k,iel) endif enddo !n 100 continue -- 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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Re: [Nek5000-users] g95 and nekton
by nek5000-users＠lists.mcs.anl.gov 11 May '10

11 May '10

Hi Andrew, cc'g to the User's list where many knowledgeable people might have insight... Particularly w.r.t. gfortran on a mac. Paul On Tue, 11 May 2010, Andrew Siegel wrote: > Paul: I give up. Do you know if we have pgf or ifort (intel) compilers that > we can install locally? > If not I'm going to buy a few. Hate having to login and move data just to do > simple runs.

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Compilation failing with gfortran
by nek5000-users＠lists.mcs.anl.gov 11 May '10

11 May '10

Hi, I'm using mpif77 with gfortran underneath and I'm not able to compile any of the examples of the latest code (which I downloaded today). The error is: /home/guest/nek5_svn/trunk/nek/navier8.f: In function 'setvert3d': /home/guest/nek5_svn/trunk/nek/navier8.f:2322: internal compiler error: in expand_expr_real_1, at expr.c:6846 Please submit a full bug report, with preprocessed source if appropriate. See <URL:http://bugzilla.redhat.com/bugzilla> for instructions. make: *** [obj/navier8.o] Error 1 However an earlier version of the code which I've been using for a couple of months works fine. Attached is the compiler.out. I've noticed that the input files are slightly different. Do we not need SESSION.NAME any more? Regards, Mani chandra

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prex & pretex not working
by nek5000-users＠lists.mcs.anl.gov 10 May '10

10 May '10

Hello, I am compiling prenek with GNU compilers, gfortran-4.3.2 and gcc-4.3.2. When I compile it without "BIGMEM" flag it gives an error, the output of it is attached (error.out). With "BIGMEM" flag turned on, there are no compiler errors (compile.out). But when I try to open pretex or prex, I get the following error. [harish@cmtl hole-in-center]$ prex Killed [harish@cmtl hole-in-center]$ pretex Killed All the other tools are working fine. Any help in solving this issue is appreciated. Thanks, Harish.

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Warning Message : L1/L2 DIV(V)
by nek5000-users＠lists.mcs.anl.gov 10 May '10

10 May '10

Dear Developers, I am trying to run an LES in a turbine blade passage and I ran into this warning message during my production run: L1/L2 DIV(V) : 1.9224E-01 2.3951E+00 L1/L2 QTL : 1.9180E-01 2.3014E+00 L1/L2 DIV(V)-QTL: 4.3317E-04 6.6792E-01 WARNING: DIV(V)-QTL too large! I tried to grep it to the source code and found that the quantity QTL refers to the thermal divergence ( I do use usrdiv in my outlet ). But my case is purely from a fluids perspective and does not involve heat transfer. So I am wondering how QTL would pop up in my simulation. And I also noted that the error message comes up only when I use PN-PN basis function. I would like to know if this error message is a concern at all . Regards Shriram

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Re: [Nek5000-users] History points
by nek5000-users＠lists.mcs.anl.gov 07 May '10

07 May '10

P.S. Yes, Frank, the exact coordinates of the history points are written only when the code rans. But if for history points you choose the collocation points on the boundary of a spectral element -- those that have I,J,K equal to either 1 or lx1 -- than you can find out their coordinates from .rea ASCII file after the line *** MESH DATA *** where coordinates of the element edges are written. Aleks ----- Original Message ----- From: nek5000-users(a)lists.mcs.anl.gov To: nek5000-users(a)lists.mcs.anl.gov Sent: Wednesday, May 5, 2010 4:45:11 PM GMT -06:00 US/Canada Central Subject: Re: [Nek5000-users] History points Hi Aleks, My question is what is the logfile? Perhaps you mean the output that NEK writes to the screen? If so, then one would know the location of the point at which data is being dumped only after entering the i,j,k and element # of the point in the *.rea file.... Cheers, Frank On Wed, 2010-05-05 at 23:37 +0200, nek5000-users(a)lists.mcs.anl.gov wrote: > Thanks Aleks. > Concerning grep, it is a linux command that searches for the string > History in the logfile. > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -- 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… _______________________________________________ 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] History points
by nek5000-users＠lists.mcs.anl.gov 06 May '10

06 May '10

Hi Frank, If you run Nek5000 with a script like nek5_svn/trunk/tools/scripts/nekb or nek5_svn/trunk/tools/scripts/nekbmpi the output will be redirected in a file blah.log* and linked to logfile. It is convenient to navigate the logfile (and the code) with unix/linux command 'grep', e.g. grep "C=" logfile shows CFL versus time, etc. Use man grep to see all the options for the command grep. Best, Aleks ----- Original Message ----- From: nek5000-users(a)lists.mcs.anl.gov To: nek5000-users(a)lists.mcs.anl.gov Sent: Wednesday, May 5, 2010 4:45:11 PM GMT -06:00 US/Canada Central Subject: Re: [Nek5000-users] History points Hi Aleks, My question is what is the logfile? Perhaps you mean the output that NEK writes to the screen? If so, then one would know the location of the point at which data is being dumped only after entering the i,j,k and element # of the point in the *.rea file.... Cheers, Frank On Wed, 2010-05-05 at 23:37 +0200, nek5000-users(a)lists.mcs.anl.gov wrote: > Thanks Aleks. > Concerning grep, it is a linux command that searches for the string > History in the logfile. > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -- 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… _______________________________________________ Nek5000-users mailing list Nek5000-users(a)lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users

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Reading binary data
by nek5000-users＠lists.mcs.anl.gov 06 May '10

06 May '10

Dear Neks, I have written a small Matlab function to read in the binary result files. Mostly I understood the structure including the header and the structure of the data. After reading in the data (in my case I only wrote x,y,z,u,v,w,p) there was still some information in the result file. See % ??? for i=1:252 rest(i)=fread(fid,1,'float'); end in the function. Can you explain me what is this?? I added the Matlab function. Best , Fred

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