[Nek5000-users] Vanishing Jacobian error description

Wed Apr 21 11:29:34 CDT 2010

Hi Michael,

That indeed sounds like a potentially very useful path to getting
geometries into NEK.  Definitely interested in more details.

Cheers,
Frank

On Wed, 2010-04-21 at 10:48 -0500, nek5000-users at lists.mcs.anl.gov
wrote:
> Paul,
> 
> I figured out the issue, and it was a mistake in the routine I was
> using to put the elements midside nodes in the correct locations. I
> fixed the issue and you can see the attached result case and image if
> you (or anyone) would like.
> 
> I should note that this geometry, although simple, was created by:
> 
> 1.  Modeled in Solidworks  
> 2.  Imported into Gambit
> 3. Meshed in Gambit
> 4. Run through our matLab code to generate rea file
> 
> This is the result, a proof of concept.  If you think there would be
> significant interest I can post a separate email to the user list, so
> it is not buried in this "vanishing Jacobian" topic.
> 
> Regards,
> Michael
> 
> ----- Original Message -----
> From: nek5000-users at lists.mcs.anl.gov
> To: nek5000-users at lists.mcs.anl.gov
> Sent: Wednesday, April 21, 2010 10:07:52 AM GMT -06:00 Guadalajara /
> Mexico City / Monterrey
> Subject: Re: [Nek5000-users] Vanishing Jacobian error description
> 
> Hi Paul,
> 
> Yes I am checking it right now. The midside nodes on the top layer and
> bottom layer are working, however the elements in the layers between
> are not. They are all generated the same way, so at the moment I'm not
> sure. 
> 
> When I remove the curved side section in the rea, it works both for
> the fine and coarse lofts. I'm not sure why it doesn't like the
> midpoints; it's almost as if it is placing them in the wrong place and
> fitting a parabola that interferes with surrounding geometry.  I'll
> look into it more here and post again when I have an update.
>  
> Thanks Paul
> 
> - Michael
> 
> ----- Original Message -----
> From: nek5000-users at lists.mcs.anl.gov
> To: nek5000-users at lists.mcs.anl.gov
> Sent: Wednesday, April 21, 2010 10:00:29 AM GMT -06:00 Guadalajara /
> Mexico City / Monterrey
> Subject: Re: [Nek5000-users] Vanishing Jacobian error description
> 
> Michael, I looked at this for a couple of different N. nek/postx think
> that the geometry is messed up --- see
> www.mcs.anl.gov/~fischer/zzz.jpg That being said, it could easily be a
> problem w/ the midside node support that I added last month. (NOTE: to
> see the geometry I had to fix something in the nek code -- normally
> when you get vanishing jacobian the code will output "xyzblah.fld01"
> with the geometry, so that you can then look at this in postx or
> visit. For pn/pn, this was broken but is now working in the
> just-updated repo.) Do you have a way to verify that your lofting is
> working? Paul On Wed, 21 Apr 2010, nek5000-users at lists.mcs.anl.gov
> wrote: > Hi, > > Sorry, yes that was for without the curve side data.
> Here is the case that includes the curved side data. > > - Michael > >
> ----- Original Message ----- > From: nek5000-users at lists.mcs.anl.gov >
> To: nek5000-users at lists.mcs.anl.gov > Sent: Wednesday, April 21, 2010
> 8:39:38 AM GMT -06:00 Guadalajara / Mexico City / Monterrey > Subject:
> Re: [Nek5000-users] Vanishing Jacobian error description > > The case
> you sent runs fine.... is it w/ or w/o the curved side info? Paul On
> Wed, 21 Apr 2010, nek5000-users at lists.mcs.anl.gov wrote: > > > 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 at lists.mcs.anl.gov > To: "Nekton User List" > Sent:
> Tuesday, April 20, 2010 3:36:44 PM GMT -06:00 U S/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 at 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+0 0 >> 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 >> >> >> >> >> >> >
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-- 
Frank Herbert Muldoon, Ph.D. Mechanical Engineering
Technische Universität Wien (Technical University of Vienna)
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