[Nek5000-users] Vanishing Jacobians while using moving mesh

[nek5000-users at lists.mcs.anl.gov]

Pradeep,

Which version of Visit are you using?  We have experienced similar
issues with version 2.4 when viewing 2D meshes.  If this is the case,
try using 2.3.2 and see if you have the same problem.

Josh

On Tue, Feb 14, 2012 at 8:08 AM,  <nek5000-users at lists.mcs.anl.gov> wrote:
> Hi Neks,
>
> I'm trying to simulate 2D flow over an oscillating cylinder using moving
> mesh, and tried to set up a test case by looking at the peris example. I
> however am getting vanishing Jacobians after the first few timesteps.
>
> I am modifying the the boundary velocity of the cylinder in userbc instead
> of userchk (as in the peris example). Would it be possible for you to look
> at my .usr file and tell me what I am doing wrong?
>
> I have attached the .rea, .usr, and SIZE with this mail.
>
> Further, when I try to view the mesh of the output (or the xyz fld
> outputfile) in visit, visit crashes with the following error:
> VisIt's viewer exited abnormally! Aborting the Graphical User Interface.
>
> Lastly, would it be possible to simulate moving walls with large
> deformations (i.e. where multiple elements get deformed), where the
> deformation is known ahead of time? (eg. a flapping aerofoil)
>
> Thank you for your help!
>
> Regards,
> Pradeep
>
> Extract from logfile:
>
>         60 U-PRES gmres:    100  7.5345E+42  1.0000E-02  4.0062E+57
> 6.7556E-03  1.5093E-02
>  ERROR:  alphad .le. 0 in econjp -1.31175831444004495E+179          16
>  ERROR:  alphad .le. 0 in econjp -1.31175831444004495E+179          16
>  ERROR:  alphad .le. 0 in econjp -1.31175831444004495E+179          16
>  ERROR:  alphad .le. 0 in econjp -1.31175831444004495E+179          16
>           60  DNORM, DIVEX  1.18120867781751263E+043
> 7.53448962619089522E+042
>          60   6.0000E-02  1.6697E-02 Fluid done
>      DT/DTCFL/DTFS/DTINIT   0.635E-45   0.635E-45   0.000E+00   0.100E-02
> Step     61, t= 6.0800000E-02, DT= 8.0000000E-04, C=******* 2.2667E-01
> 1.8287E-02
>              Solving for fluid
>
>
>     3  ERROR:  Vanishing Jacobian near      2th node of element         3.
>
>
>     2  ERROR:  Vanishing Jacobian near      2th node of element         1.
>   2.27348348709230109E+081 -5.12478988977734591E+080
>  -2.60483379627720531E+079  3.21465902039155941E+039
>     3 xyz:  -5.30056E+39  -5.84642E+39
>     3 xyz:  -5.24850E+39  -6.93109E+39
>
>
>     3  ERROR:  Vanishing Jacobian near      2th node of element         4.
>     2 xyz:   1.25061E+38   4.64957E+39
>   9.79493533554062390E+080 -3.01548938509156252E+080
>     2 xyz:  -2.46589E-08  -5.64092E-01
>
>
>     3 xyz:  -5.30056E+39  -5.84642E+39
>     3 xyz:  -5.24850E+39  -6.93109E+39
>     2  ERROR:  Vanishing Jacobian near      3th node of element         2.
>
>
>     3  ERROR:  Vanishing Jacobian near      2th node of element         5.
>   1.43125817410005932E+039 -6.03607926692375119E+038
>   5.54918579647991880E+039 -1.67302572815141788E+039
>     3 xyz:  -5.30056E+39  -5.84642E+39
>     2 xyz:  -2.46589E-08  -5.64092E-01
>     3 xyz:  -5.24850E+39  -6.93109E+39
>
>
>     3  ERROR:  Vanishing Jacobian near      2th node of element         6.
>     2 xyz:  -3.07794E-08  -7.04112E-01
>
>
>     2  ERROR:  Vanishing Jacobian near      7th node of element         7.
>   8.35923896949543198E+038 -3.55455289325888722E+038
>     3 xyz:  -5.30056E+39  -5.84642E+39
>   1.21747337192549314E+039 -1.79454406120891328E+038
>     3 xyz:  -5.24850E+39  -6.93109E+39
>     2 xyz:  -5.66434E-08  -1.29581E+00
>     2 xyz:  -6.27639E-08  -1.43583E+00
>
>
>     2  ERROR:  Vanishing Jacobian near      9th node of element         8.
>   1.17802538305091326E+039 -4.21489851051369387E+038
>     2 xyz:  -6.55671E-08  -1.49996E+00
>     2 xyz:  -3.25016E+38   4.93026E+39
>  call outfld: ifpsco: F
>
>        61  6.0800E-02 Write checkpoint:
>
>        61  6.0800E-02 OPEN:
> xyzcyl2.fld01
>  Jac error 1, setting p66=4, ifxyo=t
>
> call exitt: dying ...
>
>
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-- 
Josh Camp

"All that is necessary for the triumph of evil is that good men do
nothing" -- Edmund Burke