[Nek5000-users] Vanishing Jacobian error description

Wed Apr 21 11:25:54 CDT 2010

Hey Stefan, 

I do not know C, and I am still learning the in & outs of Fortran .  I certainly think it is possible though. I do use some built in functions that matlab offers to make my life easier, but I'm sure they can be replaced with if needed. 

Michael B, 

I'm still testing various geometries, becoming more complex each time. Our research group is using Nek with applications to Gas turbines, so our motivation to pursue this was indeed because of complex geometries.  From Solidworks , you can export as a " ParaSolid ".  You can then Import this ParaSolid into Gambit. From Gambit, I export a generic Mesh which is a . NEU (neutral file).  This is what the matLab code uses, the . neu file.  There are many middle steps, but the process seems to work. 

I think there is plenty of room for improvement, but at the moment I'm still testing new geometries. 

- Michael M. 

----- Original Message ----- 
From: nek5000-users at lists. mcs . anl .gov 
To: nek5000-users at lists. mcs . anl .gov 
Sent: Wednesday, April 21, 2010 10:52:48 AM GMT -06:00 US/Canada Central 
Subject: Re: [Nek5000-users] Vanishing Jacobian error description 

Great! 
Any chance to change your MATLAB code into C or Fortran ? 

Stefan 

On Apr 21, 2010, at 5:48 PM, 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 >> >> >> >> >> >> > _______________________________________________ > 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 
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