[Nek5000-users] Vanishing Jacobian error description

Wed Apr 21 11:04:32 CDT 2010

Michael,

I am very interested in the whole procedure.
Do you think that this could be an efficient way to generate meshes for 
complex 3D domains ?
What kind of output do you generate with Solidworks and Gambit ? .msh ?
The Matlab code has also aroused my curiosity... that could be helpful.

Regards,

Michael B.

nek5000-users at lists.mcs.anl.gov a écrit :
> 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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