[Nek5000-users] Setting up solid elements with genbox

Tue Jun 19 18:54:26 CDT 2012

Hi Kyle,

The problem looks like your .box file. You need to list the element boundaries from least to greatest. So for your lower box, reverse the order of the y-points:
-3.00 -2.96 etc

Justin

On Tue, 19 Jun 2012 18:16:03 -0500 (CDT)
nek5000-users at lists.mcs.anl.gov wrote:

> Thanks Justin. I did look at that example, and it is helpful
> (especially for setting up the boundary conditions in the .box file,
> which I have now adjusted to be blank for the fluid bc's in the solid
> domain).
> 
> My issue is that I don't understand the general steps necessary to
> setup an arbitrary domain. Simply changing the dimensions in the .box
> file, and using the conj_ht.rea as the base .rea file like this:
> 
> conj_ht.rea
> 2                      spatial dimension  ( < 0 -->
> generate .rea/.re2 pair) 2                      number of fields
> 
> Box fluid
> -8   8                                           nelx,nely for Box
> 0 8 1.                                              x0,x1,gain
> (rescaled in usrdat) -1.0 -0.96 -0.75 -0.45 0.00 0.45 0.75 0.96
> 1.00     y0,y1,...,yn P  ,P  ,W  ,W
> bc's  (3 chars each!) P  ,P  ,E  ,E
> bc's  (3 chars each!) Box upper fuel
> -8   8                                           nelx,nely for Box
> 0 8 1.                                              x0,x1,gain
> (rescaled in usrdat) 1.00 1.04 1.25 1.55 2.00 2.45 2.75 2.96 3.00
> y0,y1,...,yn ,   ,   ,                                 bc's  (3 chars
> each!) I  ,I  ,E  ,I                                 bc's  (3 chars
> each!) Box lower fuel
> -8   8                                           nelx,nely for Box
> 0 8 1.                                              x0,x1,gain
> (rescaled in usrdat) -1.00 -1.04 -1.25 -1.55 -2.00 -2.45 -2.75 -2.96
> -3.00     y0,y1,...,yn ,   ,   ,
> bc's  (3 chars each!) I  ,I  ,I  ,E
> bc's  (3 chars each!)
> 
> and then using genbox, changing nelv, deleting the fluid bc's for
> elements greater than 64, using genmap results in the peculiar error
> when running nek:
> 
>  setup mesh topology
> 
>   WARNINGa: Detected non-right-handed element.
>   Number     129  C1-4: -0.4000E-01 -0.4000E-01 -0.4000E-01
> -0.4000E-01
> 
> This is with the latest repo (843). Maybe I am missing some necessary
> changes to the .rea file?
> 
> Thanks,
> 
> Kyle
> 
> ----- Original Message -----
> From: nek5000-users at lists.mcs.anl.gov
> To: nek5000-users at lists.mcs.anl.gov
> Sent: Tuesday, June 19, 2012 3:17:21 PM
> Subject: Re: [Nek5000-users] Setting up solid elements with genbox
> 
> 
> Hi Kyle, 
> 
> Did you take a look at the conj_ht case in the examples folder? It
> has something pretty close to what you want. 
> 
> Justin 
> 
> 
> On Tue, Jun 19, 2012 at 1:18 PM, < nek5000-users at lists.mcs.anl.gov >
> wrote: 
> 
> 
> Hi all, 
> 
> I am attempting to setup a simple 2D conjugate heat transfer problem
> using genbox. I use the example "turbChannel" as my model. I want to
> setup a fluid box in between two solid boxes. Therefore, my
> 2DturbChannel.box file appears: 
> 
> base.rea 
> 2 spatial dimension ( < 0 --> generate .rea/.re2 pair) 
> 2 number of fields 
> Box 
> -8 8 nelx,nely for Box 
> 0 8 1. x0,x1,gain (rescaled in usrdat) 
> -1.0 -0.96 -0.75 -0.45 0.00 0.45 0.75 0.96 1.00 y0,y1,...,yn 
> P ,P ,W ,E bc's (3 chars each!) 
> P ,P ,W ,E bc's (3 chars each!) 
> Box 
> -8 8 nelx,nely for Box 
> 0 8 1. x0,x1,gain (rescaled in usrdat) 
> 1.00 1.04 1.25 1.55 2.00 2.45 2.75 2.96 3.00 y0,y1,...,yn 
> P ,P ,E ,W bc's (3 chars each!) 
> P ,P ,E ,W bc's (3 chars each!) 
> Box 
> -8 8 nelx,nely for Box 
> 0 8 1. x0,x1,gain (rescaled in usrdat) 
> -1.00 -1.04 -1.25 -1.55 -2.00 -2.45 -2.75 -2.96 -3.00 y0,y1,...,yn 
> P ,P ,W ,E bc's (3 chars each!) 
> P ,P ,W ,E bc's (3 chars each!) 
> 
> 
> Running genbox on this file produces a .rea file with 192 fluid
> elements. I first try to change "nelv" in the .rea file to 64.
> Running genmap on this file produces a "PERIODIC MISMATCH" error,
> likely due to the 192 boundary conditions for the fluid field. So I
> then delete all of the boundary conditions for elements greater than
> 64 in the fluid (leaving thermal boundary conditions for all 192
> elements). Genmap now works, but running nek with this .rea/.map
> combination gives the error: 
> 
> ERROR READING INITIAL CONDITION/DRIVE FORCE DATA 
> ABORTING IN ROUTINE RDICDF. 
> 
> 
> I thought that this procedure would work, given previous discussion
> on the problem of conjugate heat transfer in Nek5000
> ( http://lists.mcs.anl.gov/pipermail/nek5000-users/2010-February/000121.html
> ). Perhaps I generated the .map file from the incorrect form of
> the .rea file? My question: is there a simple way to deal with solid
> elements in this configuration without using prenek? 
> 
> Thanks, 
> 
> Kyle 
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