[Nek5000-users] to Michael--> Nek5000 & Gambit, blocked file

Mon Jun 7 11:51:34 CDT 2010

Hi Michael,

Thanks for looking at it.  After removing all boundary conditions except
the inlet and outlet and letting Gambit default everything else to walls
it runs OK.  The original flow problem is two phase with the two phases
seperated by a BC named "marangoni_interface".  If that is left out,
then I assume the boundary is set to "E", i.e., element connectivity.
If that is left in, then "Gambit2Nek" gives:

??? Attempted to access FluidBC(0,1); index must be a positive integer
or logical.

Error in ==> getBC2 at 23
        FluidBC(b,1) = Type(i);

Error in ==> rea_write at 78
FluidBC  = getBC2(ElemConn,ElmF,FaceF,TypeF,Elem1,ElemInfo);

Perhaps this is because "Gambit2Nek" cannot deal with an internal BC,
i.e., one between what were two phases?  

Also, it seems that it is not possible to give NEK bc names that have
more than 1 character?  For example; "ms" and "shl".

MOMENTUM NEK BC = ms
??? Subscripted assignment dimension mismatch.

Error in ==> readingNEU2 at 85
    type1(i) = input('MOMENTUM NEK BC = ','s');

Error in ==> rea_write at 17
[Npts,Nelm,Elem,ElemMidPts1,Pts,Elem1,ElmF,...

Cheers,
Frank

On Mon, 2010-06-07 at 10:39 -0500, nek5000-users at lists.mcs.anl.gov
wrote: 
> Hi Frank,
> 
> I think the problem is that you specified two different groups (maybe
> for a fluid & solid problem?)...at the moment, the matlab program only
> recognizes 1 fluid group from Gambit. The idea at the moment is to
> merge a fluid and solid REA using Prex. I don't know if you were
> trying to do this, but this is the first issue I see:  The Number of
> groups should be 1.
> 
> Also, For your Boundary Conditions, I see that you have marked an
> inlet and outlet, but the rest I'm not sure what they are. If they are
> simply Walls then you don't need to mark them and Gambit will label
> them as Walls by default.
> 
> - Michael
> 
> ----- Original Message -----
> From: nek5000-users at lists.mcs.anl.gov
> To: nek5000-users at lists.mcs.anl.gov
> Sent: Monday, June 7, 2010 12:30:48 AM GMT -06:00 Guadalajara / Mexico
> City / Monterrey
> Subject: Re: [Nek5000-users] to Michael--> Nek5000 & Gambit, blocked
> file
> 
> Hi Michael,
> 
> The mesh is at:
> http://tetra.fluid.tuwien.ac.at/fmuldoo/engineering-marangoni-flows/sim2/GambitToNek/simple.neu
> 
> Cheers,
> Frank
> 
> On Sun, 2010-06-06 at 08:58 -0500, nek5000-users at lists.mcs.anl.gov
> wrote:
> > Frank,
> > 
> > It is trying to extract information about the boundary conditions
> from  
> > the neu file, there is most likely an error here.
> > 
> > Attach the Neu file and I'll have a look
> > 
> > 
> > - Michael
> > 
> > On Jun 5, 2010, at 11:28 AM, nek5000-users at lists.mcs.anl.gov wrote:
> > 
> > > Hi Michael,
> > >
> > > I have been running your code and have hit the error below.
> > > Unfortunately, I don't ever use Matlab.
> > >
> > > Cheers,
> > > Frank
> > >
> > >
> > > ELEM & PTS MATRIX RESTURCTURE:    STARTED ****
> > > ??? Index exceeds matrix dimensions.
> > >
> > > Error in ==> readingNEU2 at 99
> > >        ElmF(f+1:f+n1(i),1)=BC1m(f+1:f+n1(i),1);
> > >
> > > Error in ==> rea_write at 17
> > > [Npts,Nelm,Elem,ElemMidPts1,Pts,Elem1,ElmF,...
> > >
> > >>>
> > >
> > >
> > >
> > > On Fri, 2010-06-04 at 18:42 -0500, nek5000-users at lists.mcs.anl.gov
> > > wrote:
> > >> Hi Frank,
> > >>
> > >>
> > >>
> > >> This is achieved by the step 2 in the list I gave:  You must set
> the
> > >> edge nodes from 2 to 3. Alternatively you could set the face from
> 4  
> > >> to
> > >> 8 or the volume from 8 to 20 nodes. The extra nodes that gambit  
> > >> throws
> > >> because of this are the midpoints.  For Nekton, the recent
> midside
> > >> node support feature which fits a parabola through the two corner
> > >> points and midpoint of the element side is where this comes into
> > >> play.
> > >>
> > >>
> > >>
> > >> So all you need to do is make sure you have set the mesh nodes as
> > >> above, and the matlab code does the rest. It separates the
> element's
> > >> corner nodes from the midpoint nodes. The midpoint nodes are
> written
> > >> into the curved side section of the the REA, whereas the corner  
> > >> points
> > >> are written into the Mesh data section. So...The matlab code
> only  
> > >> uses
> > >> the flag 'm' for curved side data.
> > >>
> > >>
> > >>
> > >> Also, in the inputs section you can specify a maximum radius for
> > >> consideration. The code will check each edge's corner and
> midpoints
> > >> and determine the radius curvature. If it is too large it
> considers  
> > >> it
> > >> a straight edge and moves on.
> > >>
> > >>
> > >>
> > >> Hope this helps,
> > >>
> > >>
> > >>
> > >> Michael
> > >>
> > >>
> > >> ----- Original Message -----
> > >> From: nek5000-users at lists.mcs.anl.gov
> > >> To: nek5000-users at lists.mcs.anl.gov
> > >> Sent: Friday, June 4, 2010 6:24:06 PM GMT -06:00 US/Canada
> Central
> > >> Subject: Re: [Nek5000-users] to Michael--> Nek5000 & Gambit,
> blocked
> > >> file
> > >>
> > >> Hi Michael,
> > >>
> > >> Thanks very much for the code.  One question concerning the
> curved
> > >> sides: if one had a 3D cylindrical pipe grid from Gambit, how
> would
> > >> the
> > >> curvature of the outside (boundary) faces of the grid be set in
> your
> > >> code?
> > >>
> > >> Cheers,
> > >> Frank
> > >>
> > >>
> > >> On Thu, 2010-06-03 at 21:13 -0500,
> nek5000-users at lists.mcs.anl.gov
> > >> wrote:
> > >>> Hi Frank,
> > >>>
> > >>>
> > >>>
> > >>> Try the attached.
> > >>>
> > >>>
> > >>>
> > >>> - Michael
> > >>>
> > >>>
> > >>> ----- Original Message -----
> > >>> From: nek5000-users at lists.mcs.anl.gov
> > >>> To: nek5000-users at lists.mcs.anl.gov
> > >>> Sent: Thursday, June 3, 2010 9:01:14 PM GMT -06:00 US/Canada
> Central
> > >>> Subject: [Nek5000-users] to Michael--> Nek5000 & Gambit, blocked
> > >> file
> > >>>
> > >>> Hello Michael,
> > >>>
> > >>> It seems that you sent an email with a *.zip attachment, which
> due
> > >> to
> > >>> a
> > >>> spam filter, got blocked.  If it is renamed to say *.zipp, then
> it
> > >>> should get through.
> > >>>
> > >>> Cheers,
> > >>> Frank
> > >>>
> > >>>
> > >>> -- 
> > >>> Frank Herbert Muldoon, Ph.D. Mechanical Engineering
> > >>> Technische Universität Wien (Technical University of Vienna)
> > >>> Inst. f. Strömungsmechanik und Wärmeübertragung (Institute of F 
> > >>> luid
> > >>> 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.html
> > >>>
> > >>> _______________________________________________
> > >>> Nek5000-users mailing list
> > >>> Nek5000-users at lists.mcs.anl.gov
> > >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
> > >>>
> > >>>
> > >>>
> > >>> _______________________________________________
> > >>> Nek5000-users mailing list
> > >>> Nek5000-users at 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 Fl 
> > >> uid
> > >> 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.html
> > >>
> > >> _______________________________________________
> > >> Nek5000-users mailing list
> > >> Nek5000-users at lists.mcs.anl.gov
> > >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
> > >>
> > >>
> > >>
> > >> _______________________________________________
> > >> Nek5000-users mailing list
> > >> Nek5000-users at 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.html
> > >
> > > _______________________________________________
> > > Nek5000-users mailing list
> > > Nek5000-users at lists.mcs.anl.gov
> > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
> > _______________________________________________
> > Nek5000-users mailing list
> > Nek5000-users at 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.html
> 
> _______________________________________________
> Nek5000-users mailing list
> Nek5000-users at lists.mcs.anl.gov
> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
> 
> _______________________________________________
> Nek5000-users mailing list
> Nek5000-users at 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.html